Undefended Borders

This is a pretty picture. That's Canada on the right. The border isn't very well protected—I think it's way too easy for terrorists to swim across the river from the other side. We need to build a fence.

Mythbusters

The New York Times asks whether Mythbusters is The Best Science Show on Television. Who cares? It's lots of fun even if it doesn't teach very much science. Gets my vote.

The Neville Chamberlain School of Evolutionists

Richard Dawkins writes about the "Neville Chamberlain 'appeasement' school" of evolutionists. These are scientists who are willing to compromise science in order to form an alliance with some religious groups who oppose Christian fundamentalism. Do you believe in miracles? That's okay, it's part of science. Do you believe that God guides evolution in order to produce beings who worship him? That's fine too; it's all part of the Neville Chamberlain version of intelligent design. Souls, moral law, life after death, a fine-tuned universe, angels, the efficacy of prayer, transubstantiation ... all these things are part of the new age science according to the appeasement school. There's no conflict with real science. We mustn't question these things for fear of alienating our potential allies in the fight against the IDiots. Welcome to the big tent.

Ed Brayton has declared himself one of the leading members of the Neville Chamberlain School. And now, John Lynch and Pat Hayes have joined the Ed Brayton team.

Me and PZ are on the side of science and rationalism.

Young Earth Creationsts (YEC's) and Intelligent Design Creationists (IDiots) are anti-science because they propose explanations of the natural world that conflict with science. But they're not alone in doing that. Many of the so-called Theistic Evolutionists also promote a version of evolution that Darwin wouldn't recognize. They are more "theist" than "evolutionist."

For some reason the Neville Chamberlain team is willing to attack the bad science of a Michael Denton or a Michael Behe but not the equally—and mostly indistinguishable—bad science of leading Theistic Evolutionists. Isn't that strange?

Public understanding of science will not be advanced by people like Francis Collins, Simon Conway Morris, and Ken Miller. They are subverting science in order to make it conform to their personal religious beliefs. (Which, by the way, conflict.) They are doing more harm to science than those who oppose it directly from the outside because the Theistic Evolutionists are subverting from within. It is sad that they are being supported by people who should know the difference between rationalism and superstition.

Is the appeasement strategy working? Of course not, but the most amazing thing is happening. The Neville Chamberlain School thinks it is winning in spite of the fact that leading politicians oppose evolution; most schools don't teach evolution; and the general public doesn't accept evolution. Talk about delusion. The appeasers think we should continue down the same path that led us to this situation. They think we should continue to compromise science in order to accommodate the religious moderates.

PZ Myers is only the most recent in a long list of people who have noticed that the good guys are not winning ...

Now, what is this winning strategy that Ed's Team is pushing? It seems to be more of the same, the stuff that we've been doing for 80 years, accommodating the watering down of science teaching to avoid conflict with religious superstition…the strategy that has led to a United States where a slim majority opposes the idea of evolution, and we're left with nothing but a struggle in the courts to maintain the status quo.

I don't know why this is so hard to understand. We are not winning. We are clinging to tactics that rely on legal fiat to keep nonsense out of the science classroom, while a rising tide of uninformed, idiotic anti-science opinion, tugged upwards by fundamentalist religious fervor, cripples science education. Treading water is not a winning strategy. I'm glad we're not sinking, and I applaud the deserving legal efforts that have kept us afloat, but come on, people, this isn't winning.

Hallelujah! Right on, brother.

Peer Marking

Today's Toronto Star has an interesting article on Peer Marking Gets a Negative Grade.

Students in one of our first year psychology classes were asked to submit a short writing assignment to an online evaluation program called "peerScholar." The site, which was developed by teachers at our Scarborough campus, is set up to allow papers to be graded anonomously by fellow students.

University of Toronto Teaching Assistants, represented by their union (CUPE local 3902), objected. They say this is a blatent attempt to do away with TA's in favor of a computer program. The students in the class also expressed some concern, according to the newspaper article. Apparently, students see the peer evaluation system as "inaccurate" and "unfair."

I first heard about this experiment last year when I went to a presentation by one of the authors. What impressed me was the possibility of teaching students how to critically evaluate the work of their fellow students. I was also interested in giving students some direct experience in how their grades are determined. There's no better way to learn how the system works than grading a fellow student. We did it when I was in school. As a matter of fact, I took a university course where our entire grade was based on a group discussion at the end of term where we assigned grades for each other, by consensus. But that was the 60's.

The peerScholar project seemed like a good way of introducing more participation into a course and I was/am seriously thinking of using it in my course. Here's a desrciption of how it works in the PSYA01 class. There's more information on the peerScholar discussion page. I think it's unifortunate that the authors put so much emphasis on saving money by avoiding TA's. While I recognize that's a legitimate concern, I think that peer evaluation is an important goal by itself.

I've seen the data on fairness and accuracy and it's very impressive. Students tend to be a little too hard on their colleagues but that's easy to compensate for. By the second evaluation they've become much better. If the practice were more common, the students would get much better at it. As it is, the grade assigned by the students is at least as good as that assigned by a TA. It tends to deviate more from the grade assigned by the Professors, but then so do the TA's grades.

Bill Dembski Needs Help, Again

Bill Dembski asks, ...

I suspect that the “junk DNA” hypothesis was originally made on explicitly Darwinian grounds. Can someone provide chapter and verse? Clearly, in the absence of the Darwinian interpretation, the default assumption would have been that repetitive nucleotide sequences must have some unknown function.

Fortunately, there are some smart people who post comments on Uncommon Descent. They have told Bill that the concept of junk DNA is explicitly non-Darwinian. It was proposed by scientists who didn't feel the need to explain everything as an adaptation.

I don't know how many times we've explained to Bill that not all evolutionary biologists are "Darwinists." I know I first told him four years ago but I'm sure there were others before me. He seems to be a very slow learner.

One of these years he'll realize that there's more to evolution than just natural selection.

Iraqi Children Throwing Rocks

This video from YouTube is poignant in so many ways ... It's the same situation that Canadian forces face in Afghanistan. If the children hate us then why are we there?

        

A Simple Act of Kindness

This morning I drove over to my local Tim Horton's to get a coffee. There was a lineup in the drive-through, as usual. The woman in front of me stopped by the garbage bin and tossed out an empty cup. She missed, and the cup bounced off the receptacle and rolled under her car. She opened the door a crack, peered out, saw nothing, and drove on.

I have to admit I'm really annoyed at this kind of behavior. I hate it when people throw garbage on the street, especially when there are garbage bins everywhere. I've been known to pick up litter and hand it back to the owner. Rather than drive over her discarded cup, I stopped, picked it up, and put it in the bin. I was not thinking nice thoughts when I did this and I made sure that she saw me do it.

Back in the car, I drove up to the window to get my coffee. Imagine my surprise when the server told me my coffee was free today! She informed me that the woman ahead of me had paid for my coffee.

Thanks, whoever you are. You made my day. In fact, you made my week.

City of Toronto

Here's a 360° view of Toronto.

Click here to see a larger image.

Ten Worst Science Books

John Horgan has upped the ante with his Ten Worst Science Books. I haven't read most of the ones on his list but I certainly agree with Consilience. I disagree with The Tipping Point 'cause it's not a science book and I disagree with Rock of Ages 'cause when you read it carefully you see that Gould has a valid point.

PZ Meiers adds Darwin's Black Box by Michael Behe and The Language of God by Francis Collins. I'm not sure if the Collins book qualifies as science. It's in the superstition section of my local bookstore.

John Lynch over at Stranger Fruit has an even more interesting suggestion for John Horgan's list of worst science books. Lynch would add The End of Science by John Horgan. Ouch!

I have three suggestions. The one everyone is forgetting is Icons of Evolution by Jonathan Wells. This one's a no-brainer.

One of my personal favorites is Sudden Origins: Fossils, Genes, and the Emergence of Species by Jeffrey H. Schwartz. This is a really, really, bad science book.

Another book that gets my vote is Darwin's Dangerous Idea by Daniel Dennett.

The Three Domain Hypothesis (part 2)

Jan Sapp sets the tone by outlining the history of bacterial classification and phylogenetic analysis. We’re mostly concerned with the fourth era—the one that begins in the 1990's with the publication of the first bacterial genomes.

By the late 1990's, just when the three-domain proposal and the outlines of a “universal phylogenetic tree” were becoming well established, the microbial order based on rRNA was challenged by data from complete genome analysis of bacteria. Phylogenies based on genes other than those for rRNA often indicated different genealogies, and indeed a somewhat chaotic order. The new genomic data also indicated that archaebacteria and bacteria had many genes in common: perhaps they were not that different after all.

Sapp then goes on to discuss the attack on the Three Domain Hypothesis by Ernst Mayr in an oft-quoted PNAS paper (Mayr, 1998). Mayr’s objections have more to do with classification and taxonomy than with any real dispute over the validity of the molecular data. It’s about the fact that Mayr doesn’t like cladistics. He doesn’t want molecular phylogenies to trump visible phenotypes and “common sense” (Mayr’s, of course). Mayr argues that archaebacteria and bacteria both look like bacteria so they should be lumped together in a single prokaryotic empire.

I’m not interested in that debate. If the gene trees say that archaebacteria form a separate domain then that’s good enough for me no matter how much they resemble other prokaryotes. Woese (1998) has published an adequate reply to Mayr.

The real arguments are based on conflicting gene trees and the increasingly obvious similarity between bacteria and archaebacteria at the molecular level. How do we resolve the conflicts between the ribosomal RNA trees and examples of equally well-supported trees from proteins? The first thing that comes to mind is that some of the gene phylogenies are just wrong. They are artifacts of some sort and don’t really represent the history of the genes. Most of the debate on this topic concerns the validity of the SSU trees since they are based on nucleotide sequences. It’s well-known that ribosomal RNA trees are prone to long branch attraction artifacts to a greater extend than trees based on amino acid sequences. It’s also well-known that there are some famous mistakes in rRNA trees.

For the time being, let’s assume that all genes trees are accurate representations of the gene history, bearing in mind that the opponents of the Three Domain Hypothesis are not prepared to concede that point.

Conflicting gene trees then have to be artifacts of a different sort. Some of them will accurately represent the evolution of the species while others will not. The ones that don’t follow the phylogeny of the species will deviate because the genes have a different history. Either they have been transferred singly from one species to another or they have been transferred en masse by some sort of fusion event. Sapp discusses both these possibilities.

Lateral gene transfer (LTG)—also called horizontal gene transfer (HGT)—is the latest fad in microbial evolution. You can explain away all the conflicting gene phylogenies by invoking interspecies transfer. But here’s the problem: which genes were transferred and which ones represent the “true” species phylogeny? Several papers in the book address this problem and we’ll cover them in separate postings.

Keep in mind that LGT can get you out of a messy situation but there’s a price to pay. If you envisage a time when cells were frequently swapping lots of genes to form a “net” of life, then that, in and of itself, is enough to refute the standard version of the Three Domain Hypothesis. What you’re left with is a hypothesis about the phylogeny of “some” genes and a different phylogeny for others. This gets us into playground fights about “my gene is better than your gene.” Supporters of the Three Domain Hypothesis are willing to go there in order to save the hypothesis. Do their arguments hold up?

The other way of explaining the conflict is to invoke whole genome fusions followed by selective loss of half the genes. There are several models to explain the origin of eukaryotic cells by fusion of a primitive archaebacterium with a primitive bacterium. Such an event would account for the data, which shows that most eukaryotic genes are more closely related to bacteria but some are closer to archaebacteria. There are other interesting models, for example one model postulates fusion of a primitive eukaryotic cell with a primitive bacterial cell to form the first archaebacterium! This also accounts for the data but it pretty much wipes out one of the three domains!

Most people take these fusion models seriously. If one of the fusion models is correct, then the original Three Domain Hypothesis is refuted. (One of the complications is the transfer of genes from mitochondria to the eukaryotic nucleus. We’re not talking about those genes. Those ones are relatively easy to recognize.)

Jan Sapp closes his introduction with a summary of the problems that will be addressed in the rest of the book.

... with the development of genomics, the hitherto unappreciated ubiquity of LGT was postulated to explain many gene histories other than those for rRNA. The species concept was again considered to be inapplicable to bacteria, not because of the absence of genetic recombination, as long thought, but because there seemed to be so little barrier to it. Doubts about the inability to construct bacterial genealogies arose anew because of the scrambling of the genetic record from LGT. While debates continue over which (if any) provide the most reliable phylogenetic guide, so too do debates over the origin of the eukaryotic cell nucleus and over the inheritance of acquired bacterial genomes.

---

Microbobial Phylogeny and Evolution: Concepts and Controversies Jan Sapp, ed., Oxford University Press, Oxford UK (2005)

Jan Sapp The Bacterium’s Place in Nature

Norman Pace The Large-Scale Structure of the Tree of Life.

Woflgang Ludwig and Karl-Heinz Schleifer The Molecular Phylogeny of Bacteria Based on Conserved Genes.

Carl Woese Evolving Biological Organization.

W. Ford Doolittle If the Tree of Life Fell, Would it Make a Sound?.

William Martin Woe Is the Tree of Life.

Radhey Gupta Molecular Sequences and the Early History of Life.

C. G. Kurland Paradigm Lost.

---

Mayr, E. (1998) Two Empires or Three? Proc. Natl. Acad. Sci. USA 95:9720-0823.

Woese, C. R. (1998) Default taxonomy: Ernst Mayr’s view of the microbial world. Proc. Natl. Adad. Sci. USA 95:11043-11046.

---

High School Dropouts

ABC News reports that Students Dropping Out of High School Reaches Epidemic Levels. According to the article ...

A recent study by the Department of Education found that 31 percent of American students were dropping out or failing to graduate in the nation's largest 100 public school districts.

Is 31% too high? I suspect so, but it depends on so many things. The real question—the one that's never addressed in the popular media—is, "What should be the ideal success rate in high school?" Clearly it shouldn't be zero or even 50% because we need to have public high schools that educate the majority of students to the level of high school graduate.

Should it be 100%? Of course not. It would be silly to have a situation where everyone was capable of graduating from high school. High school wouldn't mean anything. In order to be meaningful, a high school graduation diploma has to be a significant achievement and that means that some students won't succeed.

What's the ideal number? Does a 20% "dropout" rate sound about right to you? It does to me, but I'd like to hear other opinions. A 20% "dropout" rate translates to an 80% success rate. It means that the degree of difficulty of high school courses is set at a level achievable by the vast majority of students, but not all. The bar isn't too high and it's not too low. The important point is that there is a bar.

Nobel Laureates: Jacques Monod

 

The Nobel Prize in Physiology or Medicine 1965.

"for their discoveries concerning genetic control of enzyme and virus synthesis"

Jacques Monod was a biochemist who shared the Nobel prize with François Jacob and André Lwoff for their work on understanding how genes work. Part of their contribution was demonstrating that mRNA was the key intermediate between genes and proteins. Part of it was their discovery of gene regulatory sequences and repression in the lac operon. They also worked on gene regulation during bacteriophage infection of E. coli.

Monod, who was born in 1910, led a very full life. He was active in the socialist movement in France and played an important role in the French resistance during World War II. He did most of his scientific work at the Pasteur Institute in Paris after the liberation of France in 1944.

I highly recommend Monod's Nobel Lecture "From Enzyme adaptation to allosteric transitions." It reveals a state of knowlege and understanding in 1965 that most of us don't appreciate. There are figures in the lecture, especially a diagram of allosteric transitions (with "relaxed" and "stressed" conformations), that are remarkably similar to what's in modern biochemistry textbooks.

In 1971 Monod published Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology (Le hasard et la nécessité). This insightful book influenced an entire generation of scientists. Monod died in 1976.

The privilege of living beings is the possession of a structure and of a mechanism which ensures two things: (i) reproduction true to type of the structure itself, and (ii) reproduction equally true to type, of any accident that occurs in the structure. Once you have that, you have evolution, because you have conservation of accidents. Accidents can then be recombined and offered to natural selection to find out if they are of any meaning or not.

                                                                Jacques Monod (1974) p.394

Mélissa Theuriau

The voters over at digg are getting all excited about news anchor Mélissa Theuriau. I don't see why. It's just the news—old news at that. She has a funny accent. I don't think she's from Québec.

I have to admit she's better looking than Lou Dobbs.

A Picture Is Worth a Thousand Words

 

   Sometimes even

   two thousand.

   Ed, is that you? :-)

Ed Brayton Speaks

I'm going to respond to a number if things Ed Brayton says in "With Friends Like These". Let me begin by saying it doesn't really sound like I'm Ed's friend. :-)

Ed Brayton's opening attack on me refers to my tongue in check suggestion that students who reject evolution should be flunked, or not admitted to university in the first place. Anyone with a brain can recognize the humor and sarcasm in such a remark. The fact that it sets the Intelligent Design Creationists all atwitter is part of the fun.

However, behind the humor is a serious point. If students entering university have already made up their minds that evolution should be rejected, then that's a serious problem. It's not a question of ignorance. Those students have made an active decision to choose superstition over science. Given a choice of students to admit into university science programs, I would choose the ones who show some understanding of science over those who reject one the fundamental facts of biology. Wouldn't Ed?

Ed then says, ...

To be honest, I'm rapidly becoming convinced that there are two very different groups involved in fighting against the ID public relations campaign to distort science education. The distinction between the two groups is that one is fighting to prevent ID creationism from weakening science education while the other is fighting, at least in their minds, to eliminate all religious belief of any kind, even those perspectives that have no quarrel with evolution specifically or science in general, from society.

I'm mostly in the first group but I also have an interest in elminating the worst parts of religion; namely, those parts that conflict with reason. The fight against Intelligent Design Creationism and Young Earth Creationism is only part of the battle—there's a lot more involved in trying to improve science education. Some of it requires us to take a long hard look at the way science education is being eroded by well-meaning theists who don't belong in one of the obvious hard-core Creationist camps. Let's call them Theistic Evolutionists for want of a better term.

People like Ed Brayton think it's okay for Theistic Evolutionists to nibble at science and undermine its principles in subtle ways. He probably thinks it's okay because at least they aren't taking big bites. Well, Ed, I'm here to tell you that it's not all right. The little nibbles are just as bad, perhaps worse, and if you defend even a little bit of sloppy science then you are still defending sloppy science and you should be ashamed.

When Eugenie Scott and others promote a theistic version of science they seem to think they are allowing for a safe middle ground where Theistic Evolutionists like Francis Collins, Simon Conway Morris, and Ken Miller can find common cause with scientists who don't let superstition masquerade as science. They are wrong. There is no common ground between the rational and the irrational. I've written a little essay to try and explain why [Theistic Evolution: The Fallacy of the Middle Ground].

Ed continues, ...

How else to explain Moran's earlier comments here that bluntly accuse Ken Miller, the single most effective and tireless advocate of evolution and critic of ID creationism in the nation, of being anti-science merely by virtue of the fact that he attempts to reconcile science with his religious faith? In the battle Moran is fighting, theistic evolutionists are the enemy despite their advocacy of evolution, because his battle is not for evolution or against ID creationism, it is against theism, hence theists, in any form.

I'll tell you how else to explain it, Ed. I'm not a fan of religion but I'm not dogmatically opposed to religion in any form. What I'm opposed to is the attack on science by religious apologists of any stripe. You can't claim to accept evolution and then turn around and say that God is behind it all and He can tweak it whenever He wants. That's not science.

In my essay I included a diagram from a talk given by Rev. Ted Peters, a leading Theistic Evolutionist. I'll include it here.
Note that Ken Miller is way out on the left of the diagram, not far from the Intelligent Design Creationists. As a matter of fact, it's difficult to distinguish his belief from those of some Intelligent Design Creationists. Take a look at where evolutionary biology is positioned. That's where I am.

Let's not forget that this is a fight between rationalism and superstition. Science is on the side of rationalism, and so am I.