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.

Stephen Harper on Coalitions

September 9, 2004

Her Excellency the Right Honourable Adrienne Clarkson,
C.C., C.M.M., C.O.M., C.D.
Governor General
Rideau Hall
1 Sussex Drive
Ottawa, Ontario K1A 0A1

Excellency,

As leaders of the opposition parties, we are well aware that, given the Liberal minority government, you could be asked by the Prime Minister to dissolve the 38th Parliament at any time should the House of Commons fail to support some part of the government’s program.

We respectfully point out that the opposition parties, who together constitute a majority in the House, have been in close consultation. We believe that, should a request for dissolution arise this should give you cause, as constitutional practice has determined, to consult the opposition leaders and consider all of your options before exercising your constitutional authority.

Your attention to this matter is appreciated.

Sincerely,

Hon. Stephen Harper, P.C., M.P.
Leader of the Opposition
Leader of the Conservative Party of Canada

Gilles Duceppe, M.P.
Leader of the Bloc Quebecois

Jack Layton, M.P.
Leader of the New Democratic Party

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[Hat Tip: Ryan Gregory]

Intelligent Design Creationism Isn't about God

David Klinghoffer, posting on the Discovery website, says that his worldview might be attractive to atheists [What Intelligent Design Offers to Agnostics].

Intelligent design has as much to offer to the unbeliever or the unorthodox searcher as to the confirmed traditional believer. It might even have more. Does that surprise you?

Could it be a trend, with critics of intelligent design and others outside the familiar world of ID's friends and advocates at last realizing that ID isn't merely NOT the same thing as creationism? More than that, a couple have noted lately, intelligent design isn't necessarily even theistic.

Wow! That's what I call real NEWS for evolution. The idea that intelligent design might actually have nothing to do with a creator is truly astonishing.

Let's see how this plays out later on in his posting ...

Every real solution to this problem of despair assumes a reality beyond our mundane, one-dimensional and material one. How could it not? We are in despair, or fear falling into it -- whether we're religious or otherwise -- over the limitations of our own lives.

The ultimate limit is imposed by death, which we fear as no generation in memory seems to have done despite the overwhelming safety of our existence. In the meantime, while we are still alive, the lack of a sense of ultimate purpose and meaning that goes with the culture of materialism feeds the anxiety that underlies so much of that culture.

Materialism corrodes the confidence we might otherwise have that any search for meaning that we undertake is not necessarily in vain. Intelligent design offers the hope, by the refutation of materialist science, that "something is out there," whatever it might be, capable of granting genuine purpose to our existence. An agnostic like James Kirk Wall or a -- I don't know what exactly -- like Jack Scanlan should easily appreciate this.

This is why philosophy is so confusing. Let's see if I've grasped the logic here. Intelligent design is anti-materialistic but not religious. It implies the existence of "something" that is out there that gives David Klinghoffer some sort of purpose in life and makes him feel less afraid of death. That "something" can't be God because intelligent design isn't necessarily theistic.

You can't make this stuff up. All you have to do is read what the IDiots, themselves, write on the leading Intelligent Design Creationist blogs.

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Creationism Attacked in the Canadian Parliament

Yesterday the Canadian government under Stephen Harper was defeated for contempt of parliament [Canadian Government Falls]. This is the first time that this has happened in the history of the British Commonwealth.

During the debate preceding the vote, the Leader of the Bloc Québécois party, Gilles Duceppe, had this to say about the government leaders, [Hansard]

This government is very transparent. When we look at the Conservatives, we know exactly what they are thinking. We can see right through them. Quite apart from the image they like to project, if you look closely, you can see right through them. The Minister of State for Science and Technology is a creationist and believes that dinosaurs walked the earth with humans. He thinks that The Flintstones was a documentary and Dino was the star. We can see their old Reform roots, which are likely what inspired the Tea Party.

This actually resonates within the House of Commons and with Canadians. Creationists don't get much respect in Canada.

I'd definitely vote for this guy if he wasn't a separatist.

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Canadian Government Falls

This is how a parliamentary system of government works.

The following motion just passed in the Canadian House of Commons by a vote of 156-145.

Mr. Ignatieff (Etobicoke—Lakeshore) — That the House agree with the finding of the Standing Committee on Procedure and House Affairs that the government is in contempt of Parliament, which is unprecedented in Canadian parliamentary history, and consequently, the House has lost confidence in the government.

This was immediately followed by a motion from the Prime Minister to adjourn the House. That motion carried.

Michael Ignatieff, who moved lack of confidence, is the Leader of Her Majesty's Loyal Opposition (Leader of the Opposition) and the leader of the Liberal Party.

The defeat of the government on this confidence motion means that the Prime Minister (Stephen Harper) must resign. He will probably go to the Governor General (the de facto Head of State¹) and seek permission to dissolve the House of Commons and call for a general election. In the absence of any party or coalition that could command the confidence of Parliament, that request will be granted.

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1. Officially, the Governor General is the Canadian representative of the Queen of Canada who lives in the United Kingdom. The Governor General will not be phoning the Queen to ask her advice. The current Governor General is His Excellency the Right Honourable David Johnston.

How Big Is the Human Genome?

The earliest direct estimates of the size of human genome clustered around 3,000 Mb (megabase pairs) or 3.0 ×10⁹ bp (base pairs). The textbooks settled on about 3,200 Mb based mostly on reassociation kinetics. According to those results from the 1970s, roughly 10% of the genome consists of highly repetitive DNA, 25-30% is moderately repetitive and the rest is unique sequence DNA.

A study by Morton (1991) looked at all of the estimates of genome size that had been published to date and concluded that the average size of the haploid genome in females is 3,227 Mb. This includes a complete set of autosomes and one X chromosome. The sum of autosomes plus a Y chromosome comes to 3,122 Mb. The average is about 3,200 which corresonds to 3.5 pg (picograms) and that's the value on Ryan Gregory's Animal Genome Size Database.

In the past decade or so the common assumption about the size of the human genome has dropped to about 3,000 Mb. This is because the draft sequence of the human genome came in at 2,800 Mb and the so-called "finished" sequence was still considerably less than 3,200 Mb. Most people didn't realize that there were significant gaps in the draft sequence and in the "finished" sequence.

The latest information on the human genome from the human genome consortium is 3,156,105,057 bp (3,156 Mb) (Build 37 version 2, patch 2=GRCh37.p3 (November 2010)). I believe this build still has gaps around the centromeres of the chromosomes. That region consists of highly repetitive sequences that are almost impossible to clone and sequence. These regions, also known as heterochromatin, were not targets of the original sequencing project. Their total size was estimated at 198 Mb (International Human Genome Sequencing Consortium, 2004) corresponding to about 6% of the genome.

The estimate may have been too large to begin with and, in addition, I'm pretty sure that some of these heterochromatic regions are included in the total size of Build 37 v2. That means that the total size of the human genome is very likely to be ~3,200 Mb or 3.2 ×10⁹ bp.

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[Image Credit: Wikipedia: Creative Commons Attribution 2.0 Generic license]

Morton, N.E. (1991) Parameters of the Human Genome. Proc. Natl. Acad. Sci. (USA) 88:7474-7476 [free article on PubMed Central]

International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945 [doi:10.1038/nature03001]

Punctuated Equilibria

This is an old video from 1991 but it does an excellent job of explaining punctuated equilibria. That's because it features Niles Eldridge and Stephen Jay Gould.

There are two important lessons for creationists in this video. Let's hope they learn them.

1. The evidence for punctuated equilibria is based on thousands and thousands of fossils covering millions of years. It required a complete fossil record. It has nothing whatsoever to do with gaps in the fossil record. It's the exact opposite of gaps!

2. Evolution is observed when a single species splits into two species and that takes place over a relatively short period of time. "Relatively short period of time" does not mean that the new species poofs into existence. It means 50,000-100,000 years.

Whenever your creationist friends start lying to you about punctuated equilibria you can ask them to watch this video. You'd think that would stop them from spreading misinformation but then you realize that this video is 20 years old.

Facts don't seem to matter to creationists.¹

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1. In the interests of fairness, I should note that there are a great many evolutionists who also don't understand punctuated equilibria. I'm really posting this video for them and not for the creationists.

[Hat Tip: Greg Laden]

Happy St. Patrick's Day!

One of the cool things about studying your genealogy is that you can find connections to almost everyone. This means you can celebrate dozens of special days. In my case it was easy to find ancestors from England, Scotland, Netherlands, Germany, France, Spain, Poland, Lithuania, Belgium, Ukraine, Russia, United States, and, of course, Ireland.

We will be celebrating St. Patrick's Day tomorrow at the pub. It's rather hectic keeping up with all the national holidays but somebody has to keep the traditions alive!

Here's my Irish connection.¹ The shortest connection is to the parents of my grandmother. My great-grandfather was Thomas (Keys) Foster, born in County Tyrone on September 5, 1852. He immigrated to Canada in 1876. Thomas married Eliza Ann Job, born in Fintona, County Tyrone on August 18, 1852. She immigrated to Canada in 1877.

Thomas and Eliza settled in Saskatchewan in 1883 and that's where my grandmother was born. Other ancestors in this line came from the adjacent counties of Donegal (surname Foster) and Fermanagh (surnames Keys, Emerson, Moore) and possibly Londonderry (surname Job).


Happy St. Patrick's Day 2010
Happy St. Patrick's Day (2009)
Happy St. Patrick's Day (2008)
Happy St. Patrick's Day (2007)
Niall Nóigiallach - Niall of the Nine Hostages

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1. You don't have to be Irish or have Irish ancestors to celebrate St. Patrick's Day.

Five Things that Cannot Be Justified by Science

Bill Dembski thinks that in this video William Lane Craig makes a very good case against science. This is from 1998. (The other two people are atheist Peter Atkins and William F. Buckley.) Posted on Uncommon Descent: Oldie but goodie: William Lane Craig vs. Peter Atkins. Craig list five things science cannot account for. Do you believe him?



I'd probably have the same look on my face as Peter Atkins. It's not that these five things are devastating arguments against the power of science, it's that each one would take at least an hour to explain. The audience isn't going to wait that long so you know you're going to have to pass and leave Craig (and Dembski) to smugly assume that he's won.

It's typical anti-science trickery and Atkins probably wasn't expecting such a cheap shot in that environment.

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