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.

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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.

Stop the Presses: Godless Dawkins Is Subverting Schools in the UK!!

The Sunday Times in Great Britain reports that Godless Dawkins Challenges Schools.

RICHARD DAWKINS, the Oxford University professor and campaigning atheist, is planning to take his fight against God into the classroom by flooding schools with anti-religious literature.

He is setting up a charity that will subsidise books, pamphlets and DVDs attacking the “educational scandal” of theories such as creationism while promoting rational and scientific thought.

He's doing no such thing. The goal of The Richard Dawkins Foudation for Reason & Science is to promote rationality. Of course that means attacking the IDiots and religious superstition but that's just a consequence of promoting rationalism and common sense.

Here's a video where Dawkins explains his objectives.

Why the US Should Spring for a New Particle Accelerator

Harold T. Shapiro explains in SEED "Why the US Should Spring for a New Particle Accelerator". He writes, ...

The US must develop a compelling bid to host the International Linear Collider in order to safeguard American science.

Sounds good to me. It's in all our best interests that America maintain an active presence in international front-line science. Besides, it's quicker for Canadians to fly to the US than to Geneva. :-)

The photograph shows workers celebrating the connection of the first sector of the Large Hadron Collider in Geneva on November 10, 2006. It won't be long now 'till they start bashing things together. That's what physicists do these days and it cost a lot of money. Biochemists can smash things for much less money.

Noam Chomsky - What's All the Fuss About?

I've long admired Canada's decision not to participate in the war on Iraq and I've been critical of the American decision to start the war.

Whenever the topic comes up on talk.origins you can count on the resident coterie of kooks bringing up Naom Chomsky. Apparently it's a grave insult to be associated with Chomsky. I don't know whether to be insulted 'cause I'm not familiar with his writings.

Today I accidently stumbled on a link to a speech by Noam Chomsky. Here it is.



Chomsky says lot of things that make a great deal of sense to me. For example, when taking about American policy in the Middle East he says,

If somebody was watchng all of this from outer space they might be led to believe that George Bush was embedded in the White House as an agent of Osama Bin Laden. He's certainly acting that way.

With respect to Us foreign policy, ...

The US declares the sovereign right to use force as it wishes. It's gonna lead even if nobody's following.

I'm not an American but I don't see why I should feel insulted to be on the same side as Chomsky. I know many Americans who aree with what I saw in the video. Am I missing something? Is Chomsky much more evil than he appears in this clip? Is there something I should know? Is he mean to old people, or something?

Name This Molecule #2

 

Twenty-three different amino acids can be incorporated into polypeptides by the translation machinery. They all have their own codons.

The molecule on the left is one of the 23, which one?

The Greatest Science Books of All-Time

Discover magazine has published a list of The Greatest Science Books of All-Time.

I have no problem with Darwin being at the top of the list (#1 and #2) and the next six choices seem reasonable. But The Selfish Gene by Richard Dawkins at #9? No way. That book will be forgotten in a few more years. If you must put Dawkins on the list then The Blind Watchmaker is the book to pick.

The Double Helix by James D. Watson at #11 is controversial, but I have to admit it's justified. #14 is The Insect Societies by E. O. Wilson. I can't imagine who voted for that.

The top Stephen Jay Gould book is The Mismeasure of Man at #17. It's a good book but I would have put The Panda's Thumb ahead of it ... way ahead.

Some of the other choices are very strange. The most obvious omissions, in my opinion, are Chance and Necessity by Jacques Monod, The Nature of the Chemical Bond by Linus Pauling, and The Eighth Day of Creation by Horace Freeland Judson.

Neanderthal genome FAQ

I've hesitated to comment about the sequencing of Neanderthal DNA 'cause I haven't read the papers. Fortunately John Hawks has made the effort and posted the Neandertal genome FAQ. It should answer all your questions, except why John Hawks calls them "Neandertal" when Science and Nature use "Neanderthal." Personally, I prefer the original "Neanderthal."

If you want more information, Nature has a special webpage devoted to Neanderthal DNA.

They Just Don't Get It

The discussion about UCSD students being ignorant of evolution was stimulated by an article that appeared in the San Diego Union-Tribune on February 16, 2006 ["Designed to Create Controversy"]. The article quotes UCSD evolutionary biologist Joshua Kohn,

At UCSD, which is known for its strength in science and engineering, faculty members are realizing they need to pay more attention to the controversy. Two years ago, a UCSD survey found that 40 percent of incoming freshmen to the university's Sixth College – geared toward educating students for a high-tech 21st century – do not believe in evolution, said the college's provost, Gabriele Wienhausen.

The university now requires students who major in biology to complete a course in biological evolution, Kohn said. The policy became effective with freshmen who enrolled last fall. Professors had discussed the change for years, he said, but the Sixth College poll made it more urgent.

“Our own faculty has gotten sensitized to the issue that there's a bunch of people that just don't get it,” Kohn said.

If UCSD is accepting such a large number of students who don't understand one of the basic tenets of science then maybe it's time to re-examine their admissions policy? I wonder how many of the students are from Kansas?

Will the Real IDiot Please Stand up?

Bill Dembski writes, Larry Moran — Will the real idiot please stand up?. He says,

Larry Moran has been getting some play on this blog, so I’ll throw in my two cents. I met Larry in 2002, when he attended a lecture I gave at U of Toronto and confidently explained to me and the audience how indirect Darwinian pathways explain the evolution of the flagellum from the type three secretory system. To this day it amazes me that people find so bogus an argument a slam dunk for evolutionary theory. Try explaining to an engineer that the origin of the laptop computer is the product of trial and error tinkering from a cathode ray tube. If anything, this analogy fails to capture the full measure of self-delusion that evolutionary theory has become.

That's not a very accurate description of what I said. I pointed out that scientists have a pretty good explanation of irreducible complexity. In the case of the bacterial flagella, that explanation includes evolution from a more simple, primitive, secretion complex. There was good evidence for that pathway back in 2002, as I stated. The evidence is even stronger today. (See Mark Isaak's description of flagella evolution on the Talk.Origins Archive.) Is it a "slam dunk" explanation? No it isn't. We might find a better one tomorrow.

There are lots of other irreducibly complex systems that have much better evolutionary explanations. Isn't it strange that you never mention those? What I was pointing out to your audience was the fact that you did not present the views of your opponents during your talk. This is not what we expect of a seminar on a university campus. Intellectual honesty requires that we address the views disputing our favorite hypothesis. This is especially important when you are presenting the argument that irreducibly complex systems can't possibly be explained by evolution. That speculation is challenged by any known scientific explanations that have been published. You knew about those explanations but you "forgot" to mention them. In fairness, you've been more honest about this since your visit to Toronto. At least you now mention the scientific explanations in your books and lectures.

I'm sure you're well aware of the fact that irreducbibly complex systems can evolve. In fact, there are many different ways that such systems can arise by purely naturalistic means. You probably know in your heart that the main argument of the Intelligent Design Creationists has been refuted. It's time to move on, Bill. Find something else to promote your anti-science viewpoint. This one won't work any more.

Now let's talk about IDiots. You and your friends have been writing books and giving talks where you attack all professional biologists, especially the ones who have devoted their lives to studying evolution. You claim we are so stupid that we don't even realize that the fundamentals of our discipline have been proven wrong. You claim that lawyers, journalists, and mathematicians know more about evolution than researchers who have published tons of papers on evolution. You insult our intelligence, question our integrity, and denegrate our profession. You're doing it right now.

Have you heard the story about the pot and the kettle? When I call you and your friends IDiots, you're getting back a small taste of what you've been dishing out to me and my colleagues for years.