15 Questions for "Militant" Atheists

 
Oh, goody. A quiz. I love quizzes. This one comes from R.J. Eskow over at The Huffington Post [15 Questions Militant Atheists Should Ask Before Trying to "Destroy Religion"].

Here are my answers (yes, I know he didn't request answers, but what the heck; and, no, I'm not admitting to being a militant atheist, I just like quizzes) ....

1. somewhere in between
2. other forces
3. no
4. considerable
5. no
6. additional action
7. neither
8. no
9. both
10. not all and not just fundamentalists
11. yes
12. yes, no
13. both are needed
14. the latter
15. eradication of religion will improve mental health

[Hat Tip: PZ Myers, who only got 1 out of 15 correct]

Questionable Mission

 
Questionable Mission is the title of an editorial in the Washington Post. Here's an excerpt.

"THERE ARE over 25,000 Department of Defense leaders working in the rings and corridors of the Pentagon. Through Bible study, discipleship, prayer breakfasts, and outreach events, Christian Embassy is mustering these men and women into an intentional relationship with Jesus Christ," a narrator explains toward the start of a promotional video for Christian Embassy, an offshoot of Campus Crusade for Christ that focuses on diplomats, government leaders and military officers. As a uniformed Air Force Maj. Gen. Jack J. Catton Jr. explains, "I found a wonderful opportunity as a director on the joint staff, as I meet the people that come into my directorate, and I tell them right up front who Jack Catton is . . . and my first priority is my faith in God, then my family and then country. I share my faith because it describes who I am."

This is really scary. It's one of the reasons why we need to speak out against religion before it's too late.

[Hat Tip: Richard Dawkins]

Church of the Flying Spaghetti Monster Makes Front Page of The Toronto Star

 
Well, not exactly the "front"-front page. It's on the front page of the IDEAS section (Section B) of today's paper [In praise of an alternate creation theory: The Church of the Flying Spaghetti Monster gains infamy and faith.

Leslie Scrivener does a pretty good job of explaining what it's all about. The Church of the Flying Spaghetti Monster was set up to make fun of some of the arguments for the existence of God. If your argument for God also applies to the existence of the Flying Spaghetti Monster (as most do), then how good is it?

The Toronto Star even has the picture (above) of the famous Michelangelo painting that's on the ceiling of the Sistine Chapel.

I wonder what the appeasers have to say about the Flying Spaghetti Monster? I wonder if the agnostics are sincerely undecided about His existence?

Blogging

 
I'm still getting used to blogging. There are lots of tools available to help figure out what's going on. (Thanks to PZ, and others for helping me get established.)

One of the tools reveals where readers are located. This is pretty amazing. Each dot stands for someone who looked at my blog in the last few hours.

Have Humans Stopped Evolving?

Yesterday's Quirks & Quarks radio show had a segment on human evolution. Here's the description from their website:

January 6, 2007: Are Humans Still Evolving?

Evolution has made us what we are today, and we're increasingly learning what made modern humans different from our ancestors. But many scientists think that we have now removed nature's control over our genetic legacy. Our technology allows us to control our environment and survival to the degree that we may have stopped human evolution altogether. Is our growth and development as a species at a standstill? If not, what will we become in the future? Find out this week on Quirks & Quarks.

Listen to the podcast. The segment on human evolution starts about one third of the way through the show.

The idea that humans have stopped evolving is ridiculous. It reflects a deep and fundamental misunderstanding of evolutionary theory.

Fortunately, the blurb on the website doesn't reflect what was broadcast. The host, Bob McDonald actually does a very good job of sorting through the rhetoric and the show is an excellent summary of current scientific thinking. It's by far the best thing about the rate of human evolution that I've ever heard on public radio.

One of the people interviewed on the show is Steve Jones from University College, London. Jones claims that almost everyone is reproducing these days so natural selection isn't affecting humans any more. He contrasts the situation today with that in Shakespeare's time when 2 out of 3 babies didn't survive to adulthood.

This is one of the weaker parts of the show. The claim that natural selection isn't working on humans is false. It is refuted by Jones himself later on in the broadcast, and by Noell Boaz from Ross University in Dominica.

Let's deal with the increase in longevity that we've seen in some societies over the past 500 years. We'll dismiss the obvious bias in equating what happens in Caucasian societies with evolution of the entire species. What about the fact that people in London live longer today that they did in 1600? Does this have anything to do with evolution?

Jones thinks so. He says,

Now a lot of those deaths in the old days were due to genetic differences but if everybody stays alive, everybody gets through, no more natural selection.

I don't think so. It isn't obvious to me that people were surviving in 1600 because they had better genes. People died for all kinds of reasons that had nothing to do with genes. A famous example from the nineteenth century was the London cholera outbreak. In that case, you died if you were close to the contaminated Broad Street Pump and not because you had bad genes.

If you died of infection or malnutrition in 1600 it was probably due to bad luck and not bad genes. As living conditions improved, everyone benefited equally, not just those who might have been genetically susceptible. Thus, natural selection wasn't all that important back then and most of the improvements in health in developed countries have affected evolution directly. (The quibblers are waiting to pounce, so let me address two objections to that statement. First, there are other, more modern, medical advances that do affect selection—wait for them. Second, there are some examples of genetic effects on whether you survive disease. Some people might have been more resistant to the Black Plague, for example. Such examples are exceptions to the rule. The common assumption that most deaths in the past had something to do with natural selection is what I'm addressing here.)

So, let's be skeptical about the specific argument that Jones is making, namely that increased longevity, per se, is proof that the effect of natural selection is diminished in modern societies. A lot of negative selection—selection against less fit individuals—is still taking place in utero just as it always has. Lethal mutations result in spontaneous abortion or failure to produce viable sperm and eggs. This form of natural selection hasn't changed significantly. Also, even though severely handicapped children born today may survive longer, they probably won't reproduce.

On the other hand, there are medical advances that do affect natural selection. The most obvious one is the invention of eyeglasses. As Jones points out in the show, people with a genetic disposition for bad eyesight can now survive whereas back in the hunter-gatherer days it might have been much more difficult. Thus, natural selection in favor of good eyesight has been relaxed because of eyeglasses.

What does that mean for human evolution? To its credit, the Quirks & Quarks show doesn't jump to the false conclusion so common among the general public. Evolution hasn't stopped, it has increased! The removal of negative selection causes previously detrimental alleles to survive in the population; therefore, their frequency increases. Thus, evolution is happening today but was blocked by negative selection in the past.

The same argument applies to all medical advances that allow for previously handicapped individuals to survive in modern society. Human evolution is being accelerated. This is a point worth emphasizing because the opposite conclusion is so common. Most people think that removing strong negative selection means that evolution has stopped when, in fact, the exact opposite is true! The misconception arises because the general public thinks of evolution as a progressive improvement in the gene pool. Modern medicine is allowing "defective" individuals to survive. This can't be evolution according to that false understanding of evolution. (There are other things wrong with that false argument; namely, the concept that people with myopia or diabetes are somehow lesser citizens. This isn't the place to get into that discussion.)

Strong negative selection acts as a brake on evolution. It slows evolution down. Remove the brake, and evolution speeds up.

There's more to evolution than natural selection. Bob McDonald interviews Katherine Pollard from the University of California, Davis. She points out that much of evolution is due to random genetic drift. Drift has nothing to do with natural selection, so whether or not selection has decreased will play only a minor role in whether humans are evolving. You can't stop drift and you can't stop mutations. You can't stop human evolution. As McDonald puts it, "we still will evolve ... it's not the kind of evolution we imagine."

Evolution is not just the result of survival of the fittest. Furthermore, it is not progressive in spite of the fact that this misconception is widespread. As McDonald says in closing, "... this is an illusion about the way that evolution works. Evolution has never guaranteed improvement or progress, just change."

Change is good. It's good that humans are evolving. Things can only get better, right?

Abolish the Death Penalty

 
Italians are spearheading a worldwide campaign to abolish the death penalty. I support their efforts. Citizens of all countries that retain the death penalty should petition their govenrment to abolish it immediately.

The Italian government outlawed the death penalty in 1948. Whenever a death sentence is commuted, or a country abolishes capital punishment, Rome changes the color of the colosseum's lighting to deep gold. There are 68 countries that retain the death penalty. Let's try and change the colors 68 more times.

[Reuters: Rome to light Colosseum in death penalty protest][Amnesty International: Light a city for life]

Lip Balm Addiction

 
Recently some friends and relatives (you know who you are) revealed that they are "addicted" to Blistex or other lip balms.

Help is available. Lip Balm Anonymous is an organization set up to help addicts overcome their problem. Their website contains a ton of useful information about the necessity of lip balm. Many normal people need it to get through the day because otherwise they'll surely die of dry lips. Lip balm is even more important for those who can't lick their lips if their tongue is firmly planted in their cheek—like the people who created the website!

If you're still not convinced, here are Ten Signs You're Addicted to Lip Balm. Hard core addicts should take the Lip Balm Addict Quiz to see if there's any hope.

Addiction to lip balm is an urban legend. You may really, really like the taste and feel of Blistex but that's not a physical addiction. It's all in your mind. Here are some debunking sites that cover most of the myths. [Snopes, Are Lip Balms Addictive?]

There are ways of telling whether a rumor is true or not. One way is to assume that it's true and imagine the consequences. For example, let's assume that Blistix, or whatever, is physiologically addictive. If that were true, don't you think the manufacturers would have been sued by now? Wouldn't you expect to see warning labels on your tubes? In fact, wouldn't lip balms have disappeared off the shelves by now?

None of those things have happened, so you can conclude that your assumption is wrong. Either that, or there's a massive cover-up under way. But if you believe that then you've already passed beyond the stage where rationality is going to make a difference, right?

Maud Menten and the Michaelis-Menten Equation

 
The other day, when I was taking a picture of the insulin plaque on the side on my building, I also got a photo of the Maud Menten plaque at the front of the Medical Sciences Building opposite Queen's Park.

Menten is famous for the Michaelis-Menten equation

the bane of all biochemistry undergraduates.

Michaelis and Menten are responsible for establishing the fundamental principles of enzyme kinetics and for putting biochemistry on solid mathematical ground. They were never recognized by the Nobel committee for their important contributions.

Me and a Friend

 
I was cleaning up some of my files last night and I came across this photo taken in the garden of Richard Dawkins' house in Oxford last October. PZ Myers took the picture.

PZ posted a similar , but much better, photo (taken by me). I didn't have a blog back then so here it is now, better late than never. I got my copy of The God Delusion signed while I was there.

Secret Room

 
This is a photo of a door in the corridor just outside my office. I've never seen it open. What do you suppose is behind the door?

a dead Professor secret evidence that intelligent design is correct appeasers lots of dirt the Stanley Cup student lab reports that have never been graded Narnia the random genetic drift generator the graduate student lounge

Insulin Voted #1 Canadian Invention

 

CBC viewers have voted insulin the Greatest Canadian Invention. The plaque is on the side of the Medical Sciences Building where I work.

Banting and Macleod got the Nobel Prize in Physiology or Medicine in 1923. Collip and Best were excluded in one of the most notorious omissions in Nobel history.

The top ten inventions were covered on the TV show. What about the other nine? They're almost as exciting (see below). Personally, I think #10 should have been ranked much higher.

1. insulin


2. telephone


3. lightbulb


4. five pin bowling


5. wonderbra


6. pacemaker


7. Robertson screw


8. zipper


9. electric wheelchair


10. poutine

TV Ontario's Best Lecturers

 
It's time for TV Ontario's second "best lecturer" contest. The top ten finalists have been selected. Their lectures will be televised beginning January 13th. Lecturers from all over the province and from many different disciplines will be featured in the run-off.

Saturday, January 13 4:00 PM (repeated Sunday at 4:00 PM)
Jacalyn Duffin, Medicine, Queen's University
Steve Joordens, Psychology, University of Toronto at Scarborough

Saturday, January 20 4:00 PM (repeated Sunday at 4:00 PM)
Kenneth Bartlett, History, University of Toronto
Michael Persinger, Psychology, Laurentian University

Saturday, January 27 4:00 PM (repeated Sunday at 4:00 PM)
Nick Mount, English, University of Toronto
Rupinder Brar, Physics, University of Ontario Institute of Technology

Saturday, February 3 4:00 PM (repeated Sunday at 4:00 PM)
Bryan Karney, Civil Engineering, University of Toronto
Marc Fournier, Psychology, University of Toronto at Scarborough

Saturday, February 10 4:00 PM (repeated Sunday at 4:00 PM)
Allan C. Hutchinson, Law, Osgoode Hall Law School
Maydianne Andrade, Biology, University of Toronto at Scarborough

This is a popularity contest. The last one was very disappointing because some of the most important aspects of being a good university lecturer were ignored.

I'm talking about accuracy and rigour. It's not good enough to just please the students. What you are saying has to be pitched at the right level and it has to be correct. Too many of the lectures were superficial, first-year introductions that offered no challenge to the students. (One, for example, was an overview of Greek and Roman architecture by an engineering Professor.) The students loved it, of course, and so did the TV producers because they could understand the material. Lecturer's in upper level courses need not apply.

Some of last year's lectures were inaccurate. The material was either misleading or false, and the concepts being taught were flawed. Neither students nor TV audiences were in any position to evaluate the material so accuracy was not a criterion in selecting the best lecturer of 2006.

I wrote to the producers about this, suggesting that the lecturers be pre-screened by experts in the discipline. TV Ontario promised to do a better job this year. I'm looking forward to seeing if they kept their promise.

The fact that Michael Persinger is one of the finalists doesn't bode well. In case some of you don't know, Persinger is the guy who puts a motorcycle helmet full of solenoids on your head to make you become religious [This Is Your Brain on God]. Persinger used his machine to try and make Dawkins have a religious experience [God on the Brain]. It didn't work.

Persinger was not disheartened by Dawkins' immunity to the helmet's magnetic powers. He believes that the sensitivity of our temporal lobes to magnetism varies from person to person. People with TLE may be especially sensitive to magnetic fields; Prof Dawkins is well below average, it seems.

What the Heck Is Darwinian Morality?

 
John G. West is one of the chief IDiots over at the Discovery Institute. He has posted an article on Darwinism and Traditional Morality. It appears that West wrote a book about this stuff called Darwin’s Conservatives: The Misguided Quest. I haven't read it, and I don't intend to.

Here's what West says in the online article at Evolution News & Views (sic). I'm not making this up.

In my book, I challenge the attempt to locate a non-relative justification for morality in Darwinism. According to a Darwinian conception of ethics, every behavior regularly practiced by at least some subpopulation of human beings is ultimately a product of natural selection. Thus, while the maternal instinct is “natural” according to Darwinism, so is infanticide. While monogamy is “natural,” so are polygamy and adultery. Because of this uncomfortable truth, even some noted Darwinists such as Thomas Huxley have recognized the difficulty of grounding ethics in a Darwinian understanding of nature.

Huxley was no idiot. Like every other rational being, he recognizes that you can't base a code of ethics on Darwinism, or any other part of science. Talk about a strawman! What the heck goes on in the minds of these IDiots? Is it religion that makes them so stupid?

Fahrenheit 451 in 2007

 
Fahrenheit 451 is a movie about a future society where books are banned. The main protagonist is a fireman who burns books. (Apparently, books catch fire at 233°C, which translates to 451°F using the quaint, old-fashioned, way of measuring temperature that was common back in 1966.)

A new version of the movie is scheduled for 2007. Don't wait for it. If you haven't seen the Truffaut version, rush out to your video store right now and rent it. You won't regret it.

On a completely unrelated issue, () there is a movement to ban the sale of some books at the Grand Canyon National Park.


Read the full story on the NCSE website [Renewed concern about creationism at Grand Canyon National Park]. It looks like lots of people have their knickers in a knot over the sale of a creationist book that promotes Young Earth Creationism. Since the American National Park Service is a government agency, the sale of creationist books on government land is a major threat to the union.

A group called the Public Employees for Environmental Responsibility (PEER) wants the National Park Service to ban the creationist book; Grand Canyon: A Different View. The issue is complicated because it's tied up with the claim that park rangers are being muzzled by the Bush administration. There's a suggestion that rangers aren't allowed to tell visitors the real age of the Grand Canyon for fear it will insult YEC's. Wesley Elsberry does a pretty good job of getting to the truth over on The Panda's Thumb.

Of course, park rangers should promote the truth about science and the formation of the Grand Canyon. If this offends YEC's then let them go somewhere else for their vacation. (Las Vegas isn't far away.)

However, I'm troubled by book banning. I'm against it. Not only does it not make sense (have the book banners been in any other bookstore recently?), but it sends the wrong message. As a scientist, I don't fear anyone who wants to challenge science. We have truth and rationality on our side and that should be the tools we use to defeat the anti-science forces. Exposing their stupidity is part of the objective and for that we need to make their books available.

Using the law to suppress our opponents is not the best strategy. It won't achieve the objective we seek, which is to win the hearts and minds of the people. It's time to put aside the legal wranglings and concentrate on promoting rational thinking.

Reverse PIN at ATM Summons Police

 
Friday's Urban Legend

Did you get an email message like this?

I just found out that should you ever be forced to withdraw monies from an ATM machine, you can notify the police by entering your Pin # in reverse. The machine will still give you the monies you requested, but unknown to the robber, etc, the police will be immediately dispatched to help you. The broadcast stated that this method of calling the police is very seldom used because people don't know it exists. It might mean the difference between life & death. Hopefully, none of you will have to use this, but I wanted to pass it along just in case you hadn't heard of it. Please pass it along to everyone possible.

It's not true according to snopes.com, although some legislators have tried to pass laws making the reverse PIN signal mandatory. Banks don't like the idea. Besides, what are the chances that you can smoothly key in your reverse PIN number with a thug holding a gun to your head? I don't think I could. As a matter of fact, I'm not even sure I could remember my real PIN number under those circumstances!

Flying Mammals

 
Flight has been independently invented by reptiles, insects, fish, birds, and mammals. Did you know that bats aren't the only mammals that fly? Back in the 1960's every kid on the block knew about these other flying mammals.

How times have changed ....

The University Exit Exam

 
The primary goal of a university education is to teach students how to think. This is not a cliché. It really is the objective that many Professors strive for.

There are several secondary objectives—these are not universal. One goal that is widely shared is scientific literacy. We want university students to graduate with a minimal level of understanding of the natural world. Another important goal is to teach students how to express themselves in writing. We also want students to take an active interest in the world around them and learn to apply their thinking skills to current controversies.

In our free time we sometimes amuse ourselves by designing an exit exam. This is a test that all university students must pass before we give them a degree. It would require them to sit down and write 10 essays on various topics. I like the idea that they can answer any five of the questions in the morning exam from 9-12, then take a 2 hour break where they can chat with their friends about the questions, and answer the remaining five questions during the afternoon exam from 2-5.

Would you pass this exam?

Students have to write short essay answers to 10 questions. In many cases, there's no right or wrong answer. Students will be evaluated on their logic and how well they write. If they're discussing a controversial issue, the grade will depend on how well they represent both sides.

There will be a different set of questions every year. Here's an example. Can you think of any other questions that you'd like to see on the exit exam?

1. Describe and evaluate the main arguments for the existence of God(s).


2. Explain, with diagrams, how eclipses of the sun occur.


3. List ten books you have read outside of class in the past four years and tell why you liked, or didn't like, them.


4. What is your favorite music? Why?


5. What is the theory of evolution and why is it important?


6. Are you for or against abortion?


7. Is there a difference between law and justice?


8. Is socialism better than capitalism?


9. Explain earthquakes and volcanoes and how they relate to plate tectonics.


10. Is there anything wrong with genetically modified food?

ReGenesis

 
ReGenesis is a TV show produced in Mississauga, a suburb of Toronto. (I live there.) The scientific advisor is Aled Edwards, a colleague at the University of Toronto.

One of the remarkable features of the show is the reality of the biotech lab. It has all the latest equipment and gadgets and none of the scientists wear lab coats. The set was recently featured in a Toronto Star article [Putting the gee in genome].

Visit the ReGenesis website and click on "Lab Tour" then click on "NorBac Tour" to try and solve a problem using the latest biotech tools. The simulation will show you what the set looks like. The website has been nominated for several awards.

The first season's episodes are coming to The Movie Network. Watch for it.

Play the GM Quiz Game

 
How much do you know about genetically modified foods? Take the GM Quiz and find out. I scored 10/10.

[Hat Tip: Genetics & Health]

Gerald Ford

 
One of my theist friends, Denny Cochran, took this picture of the planes that flew over the Gerald R. Ford Museum in Grand Rapids during the funeral on Wednesday. The flight is following the Grand River from Lake Michigan. According to Denny, the lead planes are right over the Museum.

The services were very moving even for a Canadian. I was living in the USA when Ford became Vice-President and I always thought he was good for the country.

One of the things that surprised me about the funeral sevices in Washington was the prominent presence of the military. I guess that's to be expected when a former commander-in-chief dies.

Iraqis say they were better off under rule of Saddam Hussein

 
Iraq Centre for Research and Strategic Studies/Gulf Research Center conducted face-to-face interviews with 2,000 Iraqi adults living in major cities. The interviews were conducted in November 2006. The margin of error in such a poll is 3.1%.

According to GlobalResearch.ca the results for the question "Do you feel the situation in the country is better today or better before the U.S.-led invasion?" are:

                    Better today      5%
                    Better before    90%
                    Not sure            5%

Let's hope this puts an end to the oft-repeated myth that the Iraqis are better off after the American invasion than they were under Saddam Hussein. They don't think so.

[Hat Tip: Rhosgobel: Radagast's home]

Prostaglandin Synthesis

Eicosanoids are a class of compounds that mediate a variety of cellular responses. One group of eicosanoids is called prostaglandins. These compounds are produced by all cells and they cause the inflamatory reponse to injury and the production of pain and fever. They act like hormones and are often called hormones. They differ from true hormones in that they are produced by all cells and act locally.

Prosaglandins are made by cyclizing a 20 carbon polyunsaturated fatty acid called arachidonate. Recall that arachidonate is made from lineolate and we need to absorb linealoate from food because we can't make it ourselves. The most important reaction is the first one in the pathway. It is catalyzed by prostaglandin H synthase (PGHS) a key target for pain relief.

PGHS is a bifunctional enzyme, which means it carries out two separate reactions. The first reaction is a cyclization reaction converting arachidonate to a hydroperoxide called prostaglandin G₂. This activity is often called a cyclooxygenase (COX) activity. The second reaction is catalyzed at a different site, the hydroperoxidase site, and the final product is prostaglandin H₂.

Subsequent reactions lead to the synthesis of other prostaglandins and other eicosanoids. This is the pathway that earned Bergström, Samuelsson, and Vane the Nobel Prize in 1982.

How Painkillers Work

One way to reduce pain and fever is to inhibit prostaglandin synthesis. The ancient Greeks did this by chewing on the bark of willow trees. It turns out that willow tree bark is a natural source of salicylates and these compounds inhibit the COX acivity of prostaglandin H synthase (PGHS) by modifying the enzyme to prevent arachidonate from binding to the active site.

Unfortunately, most salicylates taste horrible and cause inflammation of the mouth, throat, and stomach. Furthermore, they block the synthesis of other prostaglandins that promote blood clotting so an excess of salicylates will lead to bleeding of ulcers and other problems.

Aspirin is a modified salicylate. The active ingredient is called acetylsalicylic acid. It was introduced as a commercial drug in 1887. It doesn't taste as bad as most other salicylates and doesn't produce severe side effects.

Although it's better than natural salicylates, aspirin can cause dizziness, ringing in the ears, and bleeding or ulcers of the stomach lining. The stomach problems are caused by inhibition of a different COX activity from the one leading to prostaglandin synthesis.

There are two different forms of PGHS or COX. COX-1 is a constitutive enzyme that regulates secretion of mucin in the stomach, thus protecting the gastric wall. COX-2 is an inducible enzyme that promotes inflammation, pain, and fever. Aspirin inhibits both isozymes.

There are many other nonsteroidal anti-inflammatory drugs (NSAIDS) that inhibit COX activity. Aspirin is the only one that inhibits by covalent modification of the enzyme. The others act by competing with arachidonate for binding to the COX active site. Ibuprofen (Advil®), for example, binds rapidly, but weakly, to the active site and its inhibition is readily reversed when drug levels drop. Acetaminophen (Tylenol®) is an effective inhibitor of COX activity in intact cells.


Physicians would like to have a drug that selectively inhibits COX-2 and not COX-1. Such a compound would not cause stomach irritation. A number of specific COX-2 inhibitors have been synthesized and many are currently available for patients. These drugs, while expensive, are important for patients with arthritis who must take pain killers on a regular basis. In some cases, the new NSAIDS have been associated with increased risk of cardiovascular disease and they have been taken off the market. X-ray crystallographic studies of COX-2 and its interaction with these inhibitors have aided the search for even better replacements for aspirin without the cardiovascular side effects.

[Modified from Horton et al. Principles of Biochemistry ©Pearson Prentice Hall]

A Confused Philosopher

Darwinism and Its Discontents, by Michael Ruse, Cambridge University Press (2006)

Ruse defines Darwinism as the idea that natural selection is the chief causal process behind all organisms (p.2). He identifies a whole list of people who oppose Darwinism. Some of these are creationists—this book is not about them.

The main "discontents," according to Ruse, are misguided social scientists with their irrational fear of genetic determinism; philosophers who "can't handle the awful truth;" and evolutionary biologists whose objections "cannot be grounded purely in theory or evidence" (p.3). Many of discontent evolutionary biologists are (gasp!) Marxists.

I am one of those scientists who question Darwinism, so this book is all about me.

What does Michael Ruse have to say about us "discontents?"

At the risk of damning myself in the eyes of sound scholarship and of God, let me be categorical. All of the critics of Darwinism are deeply mistaken.

Wrong. It is Michael Ruse who is mistaken and this damn book is full of sloppy scholarship.

Chapters 1-4 cover the basic facts of evolution. Ruse establishes the important contribution of Darwin in discovering natural selection. He points out that natural selection is the "single best idea anyone ever had" (Dennett, 195). I agree.

The "fact" of evolution is explained and the history of life is briefly described. None of this is controversial as far as scientists are concerned but Ruse is setting the stage for the most important part of the book.

Before continuing, it's worth pointing out one of the major failings of the book: the lack of any solid definition of evolution. It seems clear that Ruse is confused about the difference between evolution and one of the main mechanisms of evolution, namely, natural selection. This confusion haunts the last part of the book and makes it very difficult for Ruse to come to grips with the ideas of the "discontents."

Chapter 5 ("The Cause of Evolution") is all about natural selection. Ruse builds the case for natural selection using all the old examples that we are familiar with. Only in Chapter 6 ("Limitations and Restrictions") does he begin to address the objections to classical Darwinism.

First in the dock is adaptationism as a flawed strategy. The adaptationist fallacy is a direct frontal attack on old-fashioned Darwinian thinking. The attack was first launched by Gould and Lewontin in the famous Spandrels of San Marco paper (1979). What does Ruse have to say about this?

Now, what is to be said by the Darwinian in response to this charge? Simply this: whoever doubted the point that Gould and Lewontin are making? It has always been recognized by evolutionists—certainly from the "Origin of Species" on—that however common or ubiquitous adaptation may be, it is only part of the story. (p.135)

Bravo! In two sentences Michael Ruse admits there's more to evolution than natural selection and, therefore, the discontents have a good case. Now let's see if he understands what these other things are and why they are important. (Don't hold your breath.)

Several examples follow. In all of them, Ruse makes the case that adaptation isn't necessarily optimal. Sometimes there just hasn't been enough time for adaptation to succeed, this is why some bird species haven't yet adjusted to being parasitized by cuckoos. Sometimes natural selection has done a good, but not perfect, job; as in the circuitous route followed by mammalian sperm ducts that loop over the ureter. Sometimes natural selection is even maladaptive, as in the large antlers of the extinct Irish Elk. All of these examples are intended to show that Gould and Lewontin were wrong.

What about group selection? That's a major challenge to Darwinism and natural selection. Not a problem. Hamilton solved it by coming up with kin selection. Kin selection has been the greatest gift to adaptationist thinking since natural selection itself.

What about random genetic drift? Now, that's a real issue since there's very little doubt about its importance. (It's by far the main mechanism of evolution, properly defined.) Does Ruse agree? Nope. Ruse notes that random genetic drift was first proposed by Sewall Wright back in 1931 and expanded by Moto Kimura in 1968. But after some initial excitement Ruse concludes,

Wright's theory is not very Darwinian. Natural selection does not play an overwhelming role. Genetic drift is the key player in Wright's world. However, although many of these ideas were taken up by later thinkers, especially by Theodosuis Dobzhansky in the first edition of his influential "Genetics and the Origin of Species," drift soon fell right out of fashion, thanks to discoveries that showed that many features formerly considered just random are in fact under tight control of selection. Today no one would want to say that drift (at the physical level) is a major direct player, although in America particularly, there has always been a lingering fondness for it. (p.150)

There you have it. One of the most decisive and well studied alternatives to natural selection is dismissed as a fad. This is sloppy scholarship. Ruse clearly does not know what he's talking about. He's probably read too much of Richard Dawkins and his fellow philosopher Daniel Dennett, and not enough evolutionary biology textbooks.

Now we turn to punctuated equilibria. If Ruse is an opponent of Gould you would expect to see the standard references to saltation in this part of the book. You won't be disappointed. Although saltation and hopeful monsters have nothing to do with punctuated equilibria—and certainly nothing to do with the challenge to Darwinism—they are obligatory strawmen whenever you want to discredit Stephen Jay Gould. It's another indicator of poor scholarship.

Species selection, the real hierarchical challenge to Darwinism, isn't even mentioned. This omission is all the more remarkable since Ruse recognizes that in order to make a case for evolution at higher levels a non-Darwinian mechanism is needed; one that will decouple macroevolution and microevolution.

[Gould proposes] that at upper levels there are other mechanisms that the microevolutionists miss. Which of course might be so, but until some convincing alternatives are supplied, Darwinians continue to argue that in important respects macroevolution is microevolution writ large. Natural selection working on random mutation is the key to evolutionary change, long term as well as short term. (p.159)

What a remarkably crude way of dismissing all the work done by a large number of paleontologists, not to mention a 1433 page book called The Structure of Evolutionary Theory. Ruse may have good reason for rejecting species selection but we'll never know. Sloppy scholarship, Ruse should be ashamed.

Chapter 6 is the most important chapter since it covers the main objections of the discontented. Ruse fails to meet any of those objections; indeed, he fails to understand most of them. The rest of the book doesn't get any better.

I'll finish this off by quoting from the concluding paragraph of Chapter 6.

What is our end point? It is just plain silly to say that Darwinism is an exhausted paradigm or that selection is a trivial cause of change—or even that it calls for significant revision or augmentation. It is a powerful mechanism and has proven its worth time and time again. It is not all-powerful. Natural selection has its limits—limits that have been recognized since the time of Darwin (he himself noted many of them)—but taken as a whole, it is the key to understanding the organic world. There is no call for theory change yet, nor is there any prospect of such change in the near future. (p.165)

Speaking for the discontents, I beg to differ. Random genetic drift is by far the most common mechanism of evolution and modern evolutionary theory fully acknowledges this fact. Darwinism (natural selection) is important but it ain't the only game in town. Darwin knew nothing about random genetic drift. That's why it's wrong to describe modern evolutionary theory as Darwinism.

Gould and his colleagues have proposed a hierarchical theory of evolution in which natural selection is only one mechanism and it operates at only one level (individuals within a population). Hierarchical theory may not be correct but you'll never know from reading this damn book.

Happy Perihelion Day!

Today's the day we are closest to the sun.

It's the warmest day of the year.

Read about it on Bad Astronomy [Approaching the Sun].

You're On Notice

From The Stephen Colbert "On Notice Board" Generator. (Bears should also be on the list but I didn't have room.)

A Prayer for Appeasers

Greg Laden posted a A Boxing Day Prayer for all those who are afraid to speak out aganst supersition. I reproduce it below the fold but you need to read the complete article that goes with it on Greg's blog.

A Prayer to the Faith Based

I’m sorry, and I don’t mean to offend you,
And you didn’t even ask for this but
I’m going to put in a plug for your beliefs
So that you won’t get too mad at me as I utter words
With which you or someone you know may not agree,
(No matter how utterly wrong you may happen to be)

It is good that you are religious
And I will personally defend your right to believe
Whatever it is you do in fact believe,
And I affirm that it is OK to put
Phrases regarding your beliefs on my money
And for you to assume that
I will swear to your god

when I am on jury duty
when I am drafted into the army
when I am elected to office
when I am in the witness stand
and whenever else I must affirm
that I am moral and will not lie.

i Will Capitalize Your Word for God
And the Name of Your Holy Book
And Other Entities and Documents
As You Dictate These Rules To me.

I offer this pandering to your particular beliefs,
regardless of what they may happen to be,
despite the fact that your cultural ancestors,
the mavens and leaders of one church or another,
burned at the stake or otherwise humiliated mine,
The early scientists and freethinkers,
I affirm this because I cannot at the moment
Remember where I put my spine.

Amen.

Nobel Laureates: Bergström, Samuelsson, and Vane

The Nobel Prize in Physiology or Medicine 1982.

"for their discoveries concerning prostaglandins and related biologically active substances"

Sune K. Bergström (1916-2004), Bengt I. Samuelsson (1934-), and John R. Vane (1927-2004) received the Nobel Prize for discovering prostaglandins and working out their structure. In additon, Vane discovered the role of aspirin in inhibiting prostaglandin synthesis.

Prostaglandins are homones that mediate pain, inflamation and swelling. They also control blood clotting and and arterial constriction. See Why You need Linoleate and tomorrow's articles ("Prostaglandin Synthesis", "How Painkillers Work") for more information.

Why You Need Linoleate

Polyunsaturated fatty acids (PUFAs) are long chain fatty acids with multiple double bonds. Monday's molecule was linoleate or cis, cis -Δ^9,12- octadecadienate. It's an 18-carbon fatty acid with double bonds at positions 9 and 12. PUFA's are essential components of many biochemical pathways. (Note that this fatty acid is a normal cis fatty acid and not a trans fatty acid.)

The standard route for synthesis of PUFAs requires specific enzymes that create the double bonds at fixed positions. These enzymes are called desaturases. Other enzymes can extend the fatty acid chain from 18 carbons (18 carbons are the longest chains made by the normal fatty acid synthesis pathway). These enzymes are called elongases.

The combination of various desaturases and elongases will result in the synthesis of a wide variety of complex polyunsaturated fatty acids. One of these, arachidonate, is the precursor for synthesis of many eicosanoids—a class of compounds that includes the hormones prostaglandins, leukotrienes, and thromboxane.

Arachidonate is made from linoleate.

The first step in the pathway is activation of linoleate by attaching a cofactor called coenzyme A. The result is linoleoyl CoA, which is then converted to arachidonoyl CoA by the action of two desaturases and an elongase.


Now, here's the catch. Most eukaryotes contain a variety of desaturases that can create double bonds as far as 15 carbons away from the the carboxyl end of a fatty acid (i.e., at position 15). Mammals have lost some of these desaturase enzymes so they can't make any PUFA with a double bond beyond position 9. They (we) can't make linoleate even though it is absolutely required for life. We need to get it from our diet.

Tomorrow we'll learn how arachidonoyl-CoA is converted to prostaglandins and how aspirin, ibuprofen, acetaminophen, and other NSAIDS block the synthesis.

Shelley Batts in Toronto on New Years Eve

Shelley Batts of Restrospectacle describes her Toronto New Years and a Sad Rose Bowl. Apparently it went pretty good except that she couldn't get a cab at 3:30 am on Sunday night/Monday morning and she didn't like the Rose Bowl game.

Shelley, I can't do anything about the Rose Bowl but next time you need a cab in Toronto give me a call.

Edge Question for 2007

John Brockman runs an interesting "blog" called the Edge. He has assembled a cadre of intellectuals, and people who aspire to be intellectuals. Most of them are authors and Brockman is their agent.

This year's question is ...

The Edge Annual Question — 2007
WHAT ARE YOU OPTIMISTIC ABOUT? WHY?

As an activity, as a state of mind, science is fundamentally optimistic. Science figures out how things work and thus can make them work better. Much of the news is either good news or news that can be made good, thanks to ever deepening knowledge and ever more efficient and powerful tools and techniques. Science, on its frontiers, poses more and ever better questions, ever better put.

What are you optimistic about? Why? Surprise us!

The results are fascinating [THE WORLD'S LEADING THINKERS SEE GOOD NEWS AHEAD]. I haven't picked a favorite 'cause there are so many good ones. Many of them focus on issues that we have been discussing here: issues such as the fight between rationalism and superstition, the meaning of science, and science education.

Do you have a favorite?

Why European Countries Don't Have the Death Penalty

The recent discussion of capital punishment in another thread prompted me to look for opinion polls to see what kind of support for the death penalty there was in Europe and Canada. It turns out that a majority of citizens in those countries actually favor the death penalty in spite of the fact that their governments have abolished it.

Death penalty proponents make a big deal of this contrast. They claim that European societies are just as barbaric as American societies—although they don't actually put it in those words.

Are you interested to know how some American websites interpret this result? If so, read on, but before clicking on the "Read more" link I want to warn all Europeans that you may not like what you read. If you have high blood pressure you'd better skip it.

Here's an explanation written by Wesley Lowe on the Pro Death Penalty Webpage. Remember, he's trying to explain why European governments have abolished the death penalty in spite of the fact that a majority of Europeans support it.

Differences between European parliamentary government and the American separation-of-powers system also play a role. Parliamentary government may provide voters with more ideological variety, but it is much more resistant to political newcomers and fresh ideals which may support different political views. In parliamentary systems, people tend to vote for parties, not individuals; and party committees choose which candidates stand for election. As a result, parties are less influenced by the will of the people. In countries like Britain and France, so long as elite opinion remains sufficiently united (which, in the case of the death penalty, it has), public support cannot translate into legislative action. Since American candidates are largely independent and self-selected, they serve as a much more direct conduit between public opinion and actual political action.

Basically, then, Europe doesn't have the death penalty because its political systems are less democratic, or at least more insulated from public opinion, than the U.S. government.

This is so astonishingly ignorant that it leaves me speechless. Let's hear from other Americans on this point. Do you really believe that the government of the USA is more democratic and more open to fresh ideas than governments in Europe? Do you really believe that the US Congress is more responsive to public opinion than governments that have a parliamentary system? (While replying, keep in mind the frequency with which incumbent American politicians are turfed out of office. Contrast this with parliamentary systems where it's not uncommon for 50% of the seats to change hands in a general election.)

Brits Losing After American Invasion

According to recent reports red squirrels in Britain are facing extinction. There may be only 30,000 left in England, 10,000 in Wales, 10,000 in Northern Ireland, and 121,000 in Scotland [Red Squirrel Facts]. The European Red squirrels (Sciurus vulgaris) are being out-competed by American or Eastern gray squirrels (Sciurus carolinensis) introduced into Great Britain in 1876.

Human Brits are banding together to help the red squirrels fight off the foreign invasion [Friends of the Red Squirrel] but the prospects are dim. It looks like curtains for the reds.

This clearly has something to do with evolution. When one species out competes another and drives it to extinction we think of this as part of the process of evolution. But which process is it? It doesn't really count as natural selection, strictly defined, since that process involves differential success of individuals within a population. What do we call it when two species go head-to-head and only one survives?

Monday's Molecule #7

Name this molecule. The common name will do but there will be bonus points for finding the correct scientific name. This compound is essential in human diets. You will die if you don't get it in your food. Comments will be blocked for 24 hours. You can post your answer in the comments.

Appeaser Ed Brayton Asks Dawkins to Back Off

There's been a bit of trouble over the fact that Richard Dawkins signed a petition he shouldn't have signed. Ed Brayton attacked Dawkins and Dawkins explained that it was all a mistake.

Now, Ed Brayton has published his letter of apology to Dawkins. In that letter Brayton criticizes Dawkins for making it more difficult to oppose American creationists. This is the classic appeasement position and I'm delighted that Brayton has made his position clear. I reject it entirely. Writing to Dawkins to ask him to tone down his criticism of religion is a really, really stupid thing to do. Among other things, it shows us that Brayton doesn't understand the fight between rationalism and superstition.

It shows us something else as well. Ed Brayton needs to learn that the world does not revolve around the USA. People who live in other countries don't react well when they're told to put a muzzle on because their ideas might not play well in America.

Here's what Brayton says,

Let me address, as well, a more general subject. You and I agree on a great many things and disagree on a few. We are both staunch defenders of evolution against the ignorant attacks of creationists of every stripe, but I genuinely do believe that your aggressive anti-theism makes it more difficult for those of us engaged in the daily fight to protect science education to make our case. I hope that you understand what I believe to be the single most important aspect of this dispute, which is that the vast, vast majority of those who reject evolution do so solely because they believe it disproves their religion. The average person knows as little about evolutionary biology as I know about Sumerian architecture, which is to say virtually nothing. The only thing they know, on an almost reactive level, is that evolution = no god = no morality. Now, I think it's important to attack this misconception at the levels you do as well, by pointing out that atheism does not lead to immorality, and I make that argument loudly and often. But I assure you that for those of us "on the ground" in the battle, so to speak, every anti-theistic statement you make is amplified by our opponents and used as a sort of prophylactic to guard against the infiltration of not only evolution but of virtually all scientific thought.

I am in full agreement with Dr. Tyson, in his admonition to you at the recent Beyond Belief conference, that if you would just be more circumspect in your hostility toward religion, at least in regards to those who are largely on our side in the evolution conflict, it would help a great deal. I hope you will accept that criticism from me as graciously as you accepted it from him at the time ( and I say that with full recognition that I could also learn a thing or two about being more reserved and less bombastic from time to time). I can tell you with no hesitation that it would make my work in this regard a good deal easier and would help avoid the kinds of emotional distractions that are fed and amplified by the anti-evolution movement.

I'd like to make one more point. I find it very offensive for Ed Brayton to state that he is "on the ground" in the fight against creationism, implying that Richard Dawkins isn't. Brayton is not a scientist and he is not an expert on evolution. Yet Brayton is lecturing Dawkins on the proper strategy to pursue in order to defeat the forces of superstition and anti-science. That's hubris.

Old Professors

Jonah Lehrer is an editor for Seed magazine. On his blog, The Frontal Cortex, he has resuscitated an old argument that I though we had settled. The issue is whether Professors over 60 should be put out on an ice flow to make room for, presumably smarter, young scientists [Old Professors].

The article defines old Professors as those over 60. I'm going to assume that young Professors are under 40. Since I'm 60 years old, that makes me still middle-aged and in a good position to present a totally unbiased opinion concerning the stupidity and naivety of youth.

It might be helpful to have some examples of old dotty Professors who clearly lost all ability to contribute to science once they turned 61. In the field of evolutionary biology we have; Ernst Mayr (101 when he died last year), Jared Diamond (69), E.O. Wilson (77), Richard Dawkins (65), and Stephen Jay Gould (61 when he died in 2002).


My faculty union and the University of Toronto recently concluded an agreement to abolish mandatory retirement at age 65 and the Province of Ontario has recently passed legislation abolishing mandatory retirement in the public sector. Let's not argue about whether Professors should be forced to leave their jobs on their 65th birthday. This is a rights issue. It is ethically wrong to discriminate on the basis of age. There is no justification for such discrimination in this day and age and it's about time that we did away with it. (Most American schools abolished mandatory retirement many years ago.)

Are there any conceivable arguments for reinstating mandatory retirement that meet the test of rationality? No there aren't. So why is there still a debate?

Lehrer quotes from an article in the Boston Globe on the Graying of US Academia. The article points out that since the abolition of forced retirement, the average age of Professors is increasing (duh!) and this is a bad thing.

Why is it a bad thing? The perceived wisdom is that old Professors are taking up space that should be going to younger faculty. Well, it turns out that this isn't very significant. It will always be the case that a new faculty member will be hired every time a Professor retires. Assuming a steady state, the rate of new hires won't be much different if some of the Professors stay on past 65 or 70. (Less than 25% of Professors continue to work after they turn 65.) That argument doesn't really cut the mustard. The real problem is that the number of Professors is not expanding very much so that new opportunities for junior faculty aren't being created. In our department, for example, budget cuts are forcing us to cut back on the number of Professors.

But even if the argument were true there is no ethical way to improve the situation by getting rid of old Professors. You can't just knock on the door of Professor Dawkins and tell him to get the hell out of Oxford because there's some 32 year old post-doc who wants his job. Be reasonable, people.

There's an underlying assumption in these discussions that I find troubling. If you read John Lehrer's posting and the comments that follow, you'll see lots of discussion about whether old Professors can still do their job. Lots' of people think that young Professors are better teachers, for example. That's nonsense. I've not seen any evidence to support that assumption in my forty years of experience in universities. Some young Professors are excellent teachers and some aren't. Some old Professors are excellent teachers and some aren't.

I can tell you one thing that seems to be a general rule. Whenever we sit down as a group to discuss teaching, the older Professors bring a great deal more to the table than the younger ones. I was reminded of this last month when we discussed changes to our undergraduate and graduate programs. This is a time when wisdom counts. My older colleagues know how to effect real change and they know how to avoid fads that will get us into trouble later on. They know how to work the system for maximum benefit.

(I should point out that in science departments teaching is a minor part of the job so it doesn't play a big role in deciding whether old Professors are better than young ones.)

Administrative tasks are a major part of the average Professor's job. There's no question about the fact that the longer you've been at a university the more capable you are of handling administrative tasks. This applies to local jobs like departmental chair, associate chair, and managing undergraduate and graduate programs. It also applies to higher level jobs like chairing university committees and becoming a Dean or assistant Dean.

Research is the big bogeyman. There's this persistent myth out there that young people are ever so much better at it that the old fuddy-duddys who already have one foot in the grave. There is no evidence to support this myth, even in mathematics where it originated. If you want to maximize research productivity in a department you don't do it by forcing out highly productive scientists just because they turn 65.

Please don't misinterpret me. Of course there are old Professors who are not being productive. There are ways of encouraging them to retire and if they don't take the hint there are ways of firing them even if they have tenure. This won't be required nearly as often as people imagine, but it will happen and it should probably happen more often. On the other hand, let's not forget that there are lots of younger people who don't make the cut. It's not a direct function of age.

This is an issue that demands more sensitivity than it gets. I find it very unsettling to hear people calling for the firing of old Professors just because we need to make room for younger ones. What do you imagine those old Professors are going to do when they are fired? In many cases they have been working for much lower wages than they could have gotten in the private sector and they still have mortgages to pay and kids to put through college. They often have decent pensions but still not enough to maintain their lifestyle. (I'm not talking about Harvard, I'm talking about state schools.) Do we really want to move to a cut-throat corporate model where youth and lower wages trump wisdom and maturity? Is that the kind of university we want?

The Three Domain Hypothesis (part 6)

[Part 1][Part 2][Part 3][Part 4][Part 5]
Evolving Biological Organization
Carl Woese discovered archaebacteria and he made them fit into a separate super-kingdom, or “domain.” He is the man behind the claim that archaebacteria are so different from other bacteria that they deserve equal taxonomic status with eukaryotes. Woese is the father of the Three Domain Hypothesis, which not only claims domain-level recognition for archaebacteria, but also claims that eukaryotes descend from a primitive archaebacterium.

Back in 1995, when evidence against the Three Domain Hypothesis was mounting, I made a bet with Steven LaBonne that Woese would recant by January 1997.

I lost that bet, but eight years later Woese has finally come to his senses ... at least partly ....

I’m reviewing articles that appeared in Microbial Phylogeny and Evolution edited by Jan Sapp. Carl Woese’s contribution (“Evolving Biological Organization”) describes his current thoughts about the emergence of defined species from the pool of primitive gene-swapping cells that characterized the early history of life.

Woese’s idea, which has been evolving of a period of ten years, is that primitive life existed as a community of cells that freely exchanged genes. They shared a basic translation system for making proteins, but had little else in common. These cells evolved as a community and not as distinct lineages.

Woese refers to this time as the “progenote era” where the word “progenote” refers to a cell that has not yet established a definite link between a stable genotype and a heritable phenotype. At some point in time, certain cells make the transition from progenote to the founders of a stable lineage. The transition point is known as the “Darwinian threshold.”

The real mystery, however, is how this incredibly simple, unsophisticated, imprecise communal progenote—cells with only ephemeral genealogical traces—evolved to become the complex, precise, integrated, individualized modern cells, which have stable genealogical records. This shift from a primitive genetic free-for-all to modern organisms must by all acounts have been one of the most profound happenings in the whole of evolutionary history. Although we do not yet understand it, the transition needs to be appropriately marked and named. “Darwinian threshold” (or “Darwinian Transition”) seems appropriate: crossing that threshold means entering a new stage, where organismal lineages and genealogies have meaning. where evolutionary descent is largely vertical, and where the evolutionary course can begin to be described by tree representation. (p. 109)

According to Woese, bacteria were the first species to emerge from the pool. From that point onwards, the evolution of bacteria was “Darwinian” and could be represented by a bifurcating tree.

What about archaebacteria and eukaryotes? They emerged later ...

At that point, though, both the archaeal and eukaryotic designs remain in the pre-Darwin progenote, condition: still heavily immersed in the universal HGT field, still in the throes of shaping major features of their representative designs; and so, their evolutions cannot be represented in tree form. In other words, the node in the conventional phylogenetic tree that denotes a common ancestor of the archaea and eukaryotes does not actually exist. The two cell designs are not specifically related; it is just that the tree representation made them “sisters by default.” (p.111)

Woese suggests that the archaebacteria were the next to cross the Darwinian threshold followed by eukaryotes. This explains why archaebacteria have simpler cell components and eukaryotes are more complex. (The precursors of the eukaryote lineage spent more time in the progenote era and accumulated more innovative structures, such as nuclear membranes.)

The progenote community may have spawned other “domains” but these are now extinct, although Woese suggests there are some clues pointing to their previous existence. I assume that the progenote community itself petered out shortly after the emergence of eukaryotes.

This new theory of Woese is not very satisfying. I find the explanation somewhat confusing. Woese is trying to preserve the distinctiveness of the Three Domains while denying that their relationship can be discerned. In other words, he wants to have his cake and eat it too.

In order to defend the monophyletic domains, especially archaebacteria, he has to postulate that each one descends from a single cell, or lineage, that pops out of the progenote community. That’s why each domain has a defined root (i.e. monophyletic). But in order to account for the massive amounts of data that show eukaryotes closer to bacteria than to archaebacteria, he postulates an extended period of evolution where cells exchanged genes in a communal pool. This is not unlike the ideas of many other workers in the field except that for Woese it represents a denial of one of the basic tenets of the original Three Domain Hypothesis.

Woese is very clear about this. He makes the case that the branches at the base of the ribosomal RNA tree are not meaningful. It is wrong to assume that archaebacteria and eukaryotes share a common ancestor. I’ll close this part with an extended quote from Woese to show you just how far he’s willing to go to make the case. (Note how much he has come to agree with people like Ford Doolittle [Part 5] who have been challenging the Three Domain Hypothesis for over a decade.)

Classical biology has also saddled us with the phylogenetic tree, an image the biologist invests with a deep and totally unwarranted significance. The tree is no more than a representational device, but to the biologist it is some God-given truth. Thus, for example, we agonize over how the tree can accommodate horizontal gene transfer events, when it should simply be a matter of when (and to what extent) the evolution course can be usefully represented by a tree diagram. Evolution defines the tree, not the reverse. Tree imagery has locked the biologist into a restricted way of looking at ancestors. It is the tree image, almost certainly, that has caused us to turn Darwin’s conjecture that all organisms might have descended from a simple primordial form into doctrine: the doctrine of common descent. As we shall discuss below, it is also the tree image that has caused biologists (incorrectly) to take the archaea and the eukaryotes to be sister lineages. Much of the current “discussion/debate” about the evolutionary course is couched in the shallow but colorful and cathected rhetoric of “shaking,” “rerooting,” “uprooting,” or “chopping down” the universal phylogenetic tree. (p.102)

---

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.

---

Creation Sunday

 Looking for some entertainment in February? Check out Creation Sunday in Orangeville, Ontario (north of Toronto). On Sunday Feb. 11th and Monday Feb. 12th you can hear three of the leading IDiots from Creation Ministries International speaking on "Authority Begins With Genesis," "Genesis and the Gospel Connection," "Codes and Creation," and "What the Bible and Science say about the Age of the Earth."

It ought to be a barrel of laughs. Bring lots of popcorn.

Capital Punishment Is Barbaric

 With the hanging of Saddam Hussein, Iraq affirms its membership in the group of nations that don't deserve to be called civilized.

New But Not New

 
Another major breakthrough in molecular biology has just been reported [Jefferson researchers discover new way nature turns genes on and off]. (I've lost track of how many times traditional molecular biology has been overturned in 2006—has anyone kept a list?)

Here's the startling news,

Peering deep within the cells of fruit flies, developmental biologists at the Kimmel Cancer Center at Thomas Jefferson University in Philadelphia may have discovered a new way that genes are turned on and off during development.

Reading a bit further, we find,

According to Dr. Mazo, the researchers found that one of the likely mechanisms behind ncRNAs' ability to regulate essential coding genes is through a "transcription interference" mechanism. "Such mechanisms are known in bacteria and yeast, but not much is known in higher organisms," he explains.

In other words, it's not new at all. I've been teaching transcriptional interference during bacteriophage lambda development since 1979 and it's in many textbooks, including mine (1994).

Question: What the heck is a "higher organism?"
Answer: It's a term we look for in order to identify people who don't understand evolution.

Can You Be a Theist and Believe In Evolution?

 
John Wilkins wonders about this in God, evolution and variation. I think it all boils down to purpose. Science doesn't reveal purpose but most religions demand it. (We're talking about interventionist Gods here.) Real evolution incorporates a large degree of accident and randomness and that's just not consistent with a God who has a plan. (Yes, I'm aware of the confused rationalizations of some theistic evolutionists.)

A Challenge to Denyse O'Leary

 
Denyse O'Leary writes in Thoughts on recent books on the intelligent design controversy: Some ways to spend your holiday cash.

Case in point: North American mainstream media report that the vast majority of Americans do not believe Darwinism, with the clear implication that there must be something wrong with them. It is almost inconceivable that media boffins, for whom materialism is the normal way of thinking, would actually be interested in knowing why so many who are at liberty to doubt take up that option. And the media boffins are not likely to change. The media they govern are more likely to simply decline in importance as a source of information.

Denyse, you claim to be a journalist. I challenge you to come up with a reasonable explanation. Keep in mind that you also have to explain one additional fact; the majority of Canadians and Europeans believe in evolution and they have just as much freedom to doubt as Americans. Possibly, more.

So, give it your best shot. If you think the "media" aren't interested in knowing why so many Americans are fooled by the IDiots then here's your chance to get them interested. More importantly, here's your big chance to do what nobody else has been able to do—explain why so many people in the USA are anti-science. You could be famous.

P.S. Why are you still using the term "Darwinism" to describe acceptance of the scientific facts of evolution? You haven't been paying attention, have you?