Goodbye PZ Myers

 
There were about eighteen people at the farewell dinner for PZed and Skatje on Saturday night. We really enjoyed his visit.

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In Search of Spandrels

While looking for postings on the Maynard Smith fumble (Maynard Smith on Stephen Jay Gould) I came across this one, posted on talk.origins on Aug. 20, 1998. I had forgotten about my second search for the Spandrels paper.

This is a paper that every student of evolution should read. I can't think of a paper by Maynard Smith that falls into that category.

I recently found myself in the catacombs of the library archive far away from the stress of students writing their summer exams. It was very peaceful. It was also a place where creationists never go.

I must confess that my primary motivation for being there was work avoidance - I hate marking exams - but there was another reason as well. My secondary mission was to retrieve a pristine copy of the "Spandrels" paper so I could hand it out to my students. (My own copy had some embarassing margin notes that weren't fit for young eyes.)

There were many bound volumes of the Proceedings of the Royal Society of London (Series B). Did you know that this journal goes back over one hundred years? (That's even before I was born.) Did you know that you have to look in the stacks under "R", for "Royal", and not "P", for "Proceedings"? Did you ever wonder why librarians do that? My own theory is that they really don't want us to take out their books so they make it as difficult as possible to find something.

I was looking for volume 205 (1979). As usual, it was on the bottom shelf; way down at the level of my shoes. I had to get down on one knee and that's a lot of work. But at least volume 205 wasn't missing. With trembling hands I flipped the pages looking for the sacred text. Would it be there or would the pages have been cut out with a razor blade? Chances were good - pre-med students don't read about evolution.

Yes! There it was: "The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptionist programme" by S.J. Gould and R.C. Lewontin. They even spelled "programme" correctly! Off I went to the photocopy machine. Off I went to buy a new photocopy card. Back I came to the photocopy machine. Let's see now ... how much magnification will I need to fill an 8x11 page so I don't have to close the damn lid every time I copy a page? 125% should do it. Wrrrrr .... flash .... swish .... splat.

Maybe 120% would work ...

At last, page 598 was perfect. (Anyone want extra copies of the references from this paper?) I worked my way forward to page 581 fending off the librarian who insisted that I had to close the lid or I would ruin the photocopier - and my eyes (I'm not sure which was more important to her).

I was lucky there were three or four students to distract her. Behind my back I heard some mumblings about "eccentric" and "stubborn" but unfortunately I couldn't see exactly what was going on.

Hope I didn't miss anything interesting.

I knew that Gould had presented the paper at a meeting in London in December, 1978. Lewontin wasn't there because you have to fly to get to England and Lewontin thinks that if humans were made to fly then we would have evolved wings. So, who else was at the meeting? Did they publish papers in the same issue of the journal? Let's see ...

My thoughts were interrupted by some shouting in the line behind me. Guess I'd better get away from the photocopier. The machine seems to be making people angry.

Off I went to find a desk to sit down at. Found one. Off I went to the photocopier to retrieve my photocopy card. Back I came to the desk.

Someone was there. Found another desk. It had a banana peel on it.

Cool. All the papers are here. The meeting was called "The Evolution of Adaptation by Natural Selection" and it was organized by John Maynard Smith and R. Holliday. Orgel has a paper on evolution in vitro. The Charlesworths write about sex in plants. There's a paper by Maynard Smith on game theory and the evolution of behaviour. George Williams was present (more about him later). And guess who else? - Richard Dawkins!

The Dawkins' paper is titled "Arms races between and within species" (R. Dawkins and J.R. Krebs). It goes on and on about the adaptive significance of arms races and the optimization of animals. I bet the Gould talk was not well received by Dawkins in 1978. :-)

The Williams paper is very interesting ("The question of adaptive sex ratio in outcrossed vertebrates"). He examines two popular theories of the adaptive control of sex ratio (why there are 50% males and 50% females). After looking at the detailed models and the available data he concludes,

Evidence from vertebrates is unfavourable to either theory and supports, instead, a non-adaptive model, the purely random (Mendelian) determination of sex.

Good for him. I wish I could have been at the meeting. Maybe there was a discussion. Flipping to the back of the book I find a petulant summary of the meeting written by A.J. Cain. You can tell he's really annoyed at something that went on in the meeting,

Ever since natural selection appeared on the scene, there have been those who voiced an a priori and dogmatic dislike of it. One classic example is George Bernard Shaw ... I suspect from my own work that natural selection may have been very much more important than anyone has realized up to now. If so, can these emotional and other rejections of it, or, more generally, the tendency of the human race to take a non-objective view of evolution and kindred topics, be explained by natural selection?

There is a possible evolutionary explanation, as yet untested, and no other scientific one that I know of.

Whew! The discussion must have been exciting. Let's see, it should be right at the end. Ah, here it is,

[It has not been possible to include the general discussion in this publication.]

Damn.

Gotta go, the banana peel is making me ill - it looks like it's been here since the day before yesterday. Is that a fruit fly? Off I go.

Back again. (Forgot my pen.) See ya.

Larry Moran

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Maynard Smith on Stephen Jay Gould

 
Someone resurrected an old quotation by John Maynard Smith in a comment on Good Science Writers: Stephen Jay Gould.

Here's how I replied on March 26m 2002 on the newsgroup talk.origins. It was at least the tenth time I had addressed this silly comment by Maynard Smith.

This is not a universally held view. LAM is no doubt familiar with John Maynard Smith's famous remarks about Gould:

"Gould occupies a rather curious position, particularly on his side of the Atlantic. Because of the excellence of his essays, he has come to be seen by non-biologists as the preeminent evolutionary theorist. In contrast, the evolutionary biologists with whom I have discussed his work tend to see him as a man whose ideas are so confused as to be hardly worth bothering with, but as one who should not be publicly criticized because he is at least on our side against the creationists. All this would not matter, were it not that he is giving non-biologists a largely false picture of the state of evolutionary theory."

As an aside, isn't that beautifully written?

Genes, Memes, & Minds JOHN MAYNARD SMITH November 30, 1995, New York Review of Books (the essay was a review of "Darwin's Dangerous Idea: Evolution and the Meanings of Life" by Daniel C. Dennett).

Unfortuantely JMS drops the issue at that point and has, so far as I know, never taken it up again.

He probably thought he had better things to do.

Either that, or he was very embarrassed by his inappropriate remarks and hopes that most people will forget about them. I wonder what Maynard Smith thinks of all those idiots in the AAAS who elected Gould President of the largest scientific society in the world? What in the world could Maynard Smith have been thinking when he invited Gould to Oxford to give a prestigious series of lectures on evolutionary theory?

For those interested in the background to all this, I can do little better than suggest reading Segerstråle's book "Defenders of the Faith", where she discusses the history of all this, the arguments between people like Lewontin, E.O. Wilson, Gould, Dawkins, etc. JMS comes out of it well - he was sat in the middle trying to makes sense of both sides.

Do you really think that Maynard Smith's remarks quoted above represent someone who's trying to make sense of Gould's side? Maynard Smith is firmly on the side of Dawkins in this debate. Like Dawkins, he has never given any indication that he understands the main issues. When Maynard Smith says that Gould is presenting a "largely false picture of the state of evolutionary theory" you should appreciate that what Maynard Smith is really saying is that Gould presents a picture that Maynard Smith disagrees with. Only Maynard Smith and his friends know about the *true* picture of evolutionary theory.

Gould is not nearly as arrogant as his opponents.

I've also noted on several occasions that just because Maynard Smith can't understand the complications of modern evolutionary theory doesn't mean that his simplistic version is correct.

In addition I've pointed out that Gould is often referenced in evolution textbooks for his contributions to pluralism, heterochrony, punctuated equilibria, progression, disparity, the tape of life, species selection, and spandrels. You have to look hard to find references to Maynard Smith.

To me that suggests that Maynard Smith is a man hardly worth bothering with.

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[Image Credit: Photograph of Stephen Jay Gould by Kathy Chapman from Lara Shirvinski at the Art Science Research Laboratory, New York (Wikipedia)]

Monday's Molecule #95

 
This is a very famous molecule, featured in all biochemistry textbooks. You have to identify the molecule—be careful there are several possibilities and it's easy to go wrong. You don't have to tell me the species. (Hint: the three red amino acid side chains are aspartate, histidine, and serine.)

This week's Nobel Laureate(s) won the prize for his work with this molecule (and several others).

The first one to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are only two ineligible candidates for this week's reward: Haruhiko Ishii, and Bill Chaney of the University of Nebraska.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: The molecule is chymotrypsin, not chymotrysinogen or pepsin or elastin. These proteins are called serine proteases because they have a catalytic serine residue in the active site. The Nobel Laureate is John Howard Northrop, the first person to purify and crystallize chymotrypsin. The first person to get it right was Dima Klenchin of the University of Wisconsin, who just recently fell off the ineligible list.

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Conservatives Approve Physical Violence

 
Normally I don't pay much attention to the Blogging Tories, a group of conservative Canadian bloggers. Canadain Cynic usually does a good job of finding the most ridiculous postings so we can all have a good chuckle from time to time [see She's so adorable, with that folksy racism of hers]. The average IQ of these blogging Tories seems to be significantly below 80.

"Hunter" is a female blogger from Alberta—Canada's version of Texas. She really doesn't like Barack Obama and has taken it upon herself to warn all Canadians about the perils of socialism. Here's an example of her latest posting [Coming to America].

Are Americans going quietly into socialism? Here is a good take on freedom of speech, and the 2nd Amendment:


Kind of says it all doesn't it.

Just in case some non-Americans are confused about the reference to the 2nd Amendment, let me remind you that it's the amendment Americans use to justify their right to have guns and shoot people who disagree with them.

It does say it all. Conservatives on both sides of the border seem to think it's acceptable to shoot someone who steals campaign signs. That says a lot about their mentality. Who wants to live in a society where such people have guns?

There are days when I secretly hope that McCain wins the election. Then maybe some of our conservative citizens from Alberta could move to Texas. This would benefit both Alberta and Texas.

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Mendel's Garden #25

 
The 25th edition of Mendel's Garden has just been posted on evolgen [Mendel's Garden #25].

After a few months¹ off, here's the return of Mendel's Garden.

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1. Six, to be exact.

A New Customer for Tim Hortons

 
PZ Myers has posted a video of his daughter Skatje having breakfast at Tim Hortons.

This is the first step toward becoming Canadian. We welcome everyone, even the godless. [You Will Be Assimilated!]

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David Berlinski Says Evolution Is Wrong: Wayne Eyre of the National Post Falls for It

 

Yesterday Wayne Eyre wrote a column for the National Post entitled 'Darwin? That's just the party line'. Here's how it starts ..

For example, Richard Dawkins, author of The God Delusion, says that anyone who doesn't believe in evolution "is ignorant, stupid or insane." Oxford professor Peter Atkins, another ardent atheist, recently denounced theology, poetry and philosophy and concluded that "scientists are at the summit of knowledge, beacons of rationality and intellectually honest." Geneticist Emile Zuckerkandl -- writing on whether biological facts suggest an intelligent designer -- terms the notion of intelligent design an "intellectual virus" and its advocates "an offensive little swarm of insects ... [who] feed like leeches on irrational beliefs."

That these gentlemen go on like this in the wake of, for example, biochemist Michael Behe's masterful Darwin's Black Box, in which he sets out a devastating case for the "irreducible complexity" of human systems, truly makes one wonder about the confidence they have in their own convictions.

Anyone who would describe Behe's argument as "devestating" has obviously not been paying attention.

But this isn't a column about Behe. Instead, it's a homage to another IDiot named David Berlinski,¹ especially his recent book The Devil's Delusion: Atheism And Its Scientific Pretensions.

Now you'd expect to see a nice summary of the most powerful arguments for Intelligent Design Creationism, wouldn't you? That's not what this column is about. What impresses Wayne Eyre is all the hype about evolution being wrong and that's what he picks out from Berlinksi's book. (In fairness, that's all there is in the book.)

He's the best example that impresses Eyre.

"Suspicions about Darwin's theory arise for two reasons," he writes. "The first: The theory makes little sense. The second: It is supported by little evidence ... The theories that we do have do what they can do, and then they stop. They do not stop because a detail is missing; they stop because we cannot go on. Difficulties are accommodated by the magician's age-old tactic of misdirection."

Berlinski -- who argues that computer simulations of Darwinian evolution fail when they are honest and succeed only when they are not -- says the unpersuasiveness of the literature on the subject is well known. He tells how a Nobel laureate once said to him in a faculty lounge: "Darwin? That's just the party line."

In his dissection of Darwinists and Darwinism, Berlinski notes that "if biologists are wrong about Darwin, they are wrong about life, and if they are wrong about life, they are wrong about everything."

Little wonder, then, that so many of them do indeed protest so much.

That's it folks. David Berlinski, who is not a biologist, says that evolutionary biologists are wrong about evolution and that's all it takes to impress Wayne Eyre.

And you wonder why we call them IDiots?

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1. Described by Eyre as "a highly respected member of the scientific elite." You can't just make this stuff up ... or can you?

[Hat Tip: Canadian Cynic]

PZ Myers in Toronto

 
P.Zed¹ Myers gave a wonderful talk last night. He and his daughter Skatje arrived at 2pm and we had time for snacks and drinks at the Faculty Club before he was whisked off to the Center for Inquiry for a reception at 6pm. About 10 fans joined us at the Faculty Club.

Here's P.Zed just before his talk with Justin Trottier, Director of CFI, Ontario and Katie Kish, Assistant Director. I'll try and get another picture of PZed with Kate Fairbrother, President of the University of Toronto Secular Alliance.


Here's a fuzzy picture of P.Zed describing the Cracker Affair. There were about 500 people in the audience including some of your favorite bloggers and regular commenters. Canadian Cynic was there but he/she was well disguised—after all, it was Halloween. My friend, the Jesuit priest, was there. I'll be anxious to find out what he thought of the cracker desecration!


After the talk, about 30 people joined P.Zed and Skatje at O'Grady's Pub for a glass of water. Here's P.Zed talking to some of the people who came out to see him. That's Skatje in the background.

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P.Zed tells me that he prefers the English version of his name to the American version (P.Zee) because the English version sounds so much more sophisticated.

Proposition 8

 
Last May the California Supreme Court ruled that same-sex couples have the right to marry according to the California Constitution. Since then 16,000 same-sex couples have been married in California [California Proposition 8 (2008)].

On November 4th voters will decide on whether or not to change the California Constitution to block the marriage of same-sex partners. This is Proposition 8:

ELIMINATES RIGHT OF SAME-SEX COUPLES TO MARRY. INITIATIVE CONSTITUTIONAL AMENDMENT. Changes the California Constitution to eliminate the right of same-sex couples to marry in California. Provides that only marriage between a man and a woman is valid or recognized in California. Fiscal Impact: Over next few years, potential revenue loss, mainly sales taxes, totaling in the several tens of millions of dollars, to state and local governments. In the long run, likely little fiscal impact on state and local governments.

The latest polls indicate that the "yes" side has a slight lead. If the "yes" side wins next Tuesday, it will be illegal for same-sex couples to marry in California.

This is California, folks. In the United States of America. In the 21st century. Gay couples are getting married but that right might be withdrawn.

What the heck is going on?

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[Photo Credit: BBC News]

Tangled Bank #117

 
The latest issue of Tangled Bank has been published on Pro-Science [Tangled Bank #117].

Welcome everybody to the 117th edition of the blogosphere’s premiere science and medicine blogcarnival, Tangled Bank. Tangled Bank started out as a sort of Carnival of the Vanities for science bloggers taking it’s name from Charles Darwin’s famous metaphor:

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms.

It’s fitting that this edition should itself present such a tangled bank of blog posts intertwining many different fields of science and medicine. Unfortunately, that means it becomes almost impossible to find a common theme or even group together the posts in any meaningful way. So I’m going to take the easy way out and simply list them in no particular order, although we’ll try to group related posts together.

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Send an email message to host@tangledbank.net if you want to submit an article to Tangled Bank. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger.

The Best Invention of 2008

 
According to Time magazine it's "The DNA Retail Test." Especially the one marketed by 23andMe.

We are at the beginning of a personal-genomics revolution that will transform not only how we take care of ourselves but also what we mean by personal information. In the past, only élite researchers had access to their genetic fingerprints, but now personal genotyping is available to anyone who orders the service online and mails in a spit sample. Not everything about how this information will be used is clear yet — 23andMe has stirred up debate about issues ranging from how meaningful the results are to how to prevent genetic discrimination — but the curtain has been pulled back, and it can never be closed again. And so for pioneering retail genomics, 23andMe's DNA-testing service is Time's 2008 Invention of the Year.

1. It's not an invention. The technology has been in place for years. It depends on the work done by hundreds of labs who are investigating the human genome. They deposit their results in public databases.


2. The profit making company is emphasizing genealogy as much as health. For $1000 (now $399) you can find out how your haplotyes compare to others. This is the best invention of 2008?


3. There are serious ethical concerns about genetic testing that have not been resolved.


4. Other companies are selling tests that are just as good and The Genographic Project from National Geographic deserves just as much, if not more, credit than any private company.


5. Many of the people who buy these products are scientifically literate, and responsible, adults. But there's plenty of opportunity to exploit others who might not understand what the test means.

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What the Heck Is This?

 
You must go to Botany Photo of the Day to find out. Be thankful that we can't reproduce smells on our blogs.

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32 Nearby Stars

 
Check out this interactive star map of the 32 nearest stars [32 Nearby Stars].

Imagine that humans could establish colonies on several of these stars in the next 10,000 years. This means that we would have reached out 10 light years in that time. Continuing at that pace, in one million years we would have colonies that are 1000 light years away. In one hundred million years we will have covered more than half the galaxy.

If there are other civilizations like ours, they would have to be less than one hundred million years older than us or they would likely be here by now. Maybe we are alone in the galaxy/universe?

UPDATE: I've been reminded that this argument against the high probability of life is known as the Fermi Paradox.

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[Hat Tip: Bad Astronomy]

On Assuming that God Obeys the Laws of Physics and Chemstry

 
John Pieret admires a recent posting by Steven Novella on NeuroLogica Blog where he (Novella) writes about More on Methodological Naturalism.

This methodoligical approach also deals with the problem of whether or not science can deal with God. The answer is - yes and no. If a supernatural (meaning inaccessible to science) power were meddling with our universe (with stuff science could access), science could detect it, document it, and even describe it. We could say that something was happening.

However (by the premises of this hypothetical situation) if the ultimate cause of these physical effects were beyond scientific methodology, the best science could do would be to describe anomalies. Science comes across anomalies all the time, and the typical approach is to assume (because we really have no choice) that the anomalies are due to either errors in observation, errors in our current theories, or incompleteness in our current theories, meaning there is some new phenomenon to discover.

So far the scientific approach (assuming anomalies will lead to a deeper understanding of reality) has worked out pretty well. This is the best evidence we have that our universe if mostly rational and does not include “supernatural” (by my definition) forces that will remain forever “mysterious.” If it did, then we would run across anomalies that we could never explain scientifically. All we could do would be to describe them, but we could never come up with a testable theory of mechanism.

I pretty much agree with what Steven Novella says here, although I note that he gets a bit fuzzy in other parts of the same posting. The basic point is that scientists are capable of detecting things that are not explainable by naturalistic explanations. In other words, if something isn't obeying the laws of physics and chemistry,¹ then we''ll know about it, even if we have to put it down as an unexplained anomaly.

The fact that there aren't any known mysteries that fall into this category means that there is no evidence for a God that acts in a supernatural manner. This is not the God of Francis Collins. Collins is a scientist who presents "evidence" that God exists.

The fact that most other scientists do not find such evidence is not proof that all types of God don't exist. It merely defines limits to the types of God that are possible if you use scientific reasoning.

John Pieret seems to knows this since in his posting Natural Method he asks:

I would quibble that divine action would not necessarily produce anomalies. For example, how could we tell the difference between a random mutation and a miraculous one?

Claiming that we can see no pattern in mutations, or the evolution it powers, does no good because that requires that you make an assertion about what God wants to do and how he, she or it would go about it -- and how could you know that?

John is doing exactly what he says is wrong. In light of the fact that several testable hypotheses about God have been refuted, John then speculates about what God might be doing to get around the conflict between science and religion. He imagines that God could, if he so wished, disguise his actions so that they were indistinguishable from actions that were entirely natural.

None of us can refute that possibility but I note that the goalposts have moved just about as far as they can go. We're left with a God who is so careful to avoid revealing himself that he might as well not exist. What's the point?

Why in the world did anyone start believing in such a God in the first place?²

If we weren't talking about religion, this kind of "logic" would be quickly dismissed. Imagine, for example, that someone claimed the stock market was being manipulated by clever gremlins. Pointing out that there was no evidence of such manipulation provokes the response, "These are very clever gremlins who go to extraordinary lengths to disguise their manipulations. That's why we can't detect them."

Since we can't disprove the existence of such gremlins, is that a reason to believe in them? Should we treat the gremlin-believers in the same way that we treat everyone else or are we right to be a little concerned about their psychological well-being? Is it okay to tentatively conclude that they are deluded?

Why does belief in God always get special privileges that we never grant to any other superstitions?

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1. It's a metaphor, John, not the be taken literally.

2. The answer, of course, is that nobody ever believed in such a God. This sort of God is merely the last refuge of those who used to believe in a personal, interventionist God but now find that they can't defend such a belief in a modern skeptical society. It's also the fallback position for those strange people who call themselves true agnostics. They have almost as much at stake in trying to show that we can't "prove" the nonexistence of God. They desperately want to avoid being a non-believer (atheist).