Understanding Intelligent Design

 
Dembski's latest book Understanding Intelligent Design is now on sale. Here's what Dembski has to say about it on his blog [Understanding Intelligent Design — now available at Amazon.com!].^1.

The book is geared at Christian young people (junior high and high schoolers) as well as for Church groups (e.g., Sunday Schools) to help get out the word about ID — specifically WHAT IS IT? WHY IS IT IMPORTANT? and WHAT YOU CAN DO ABOUT IT?

I was particularly concerned in writing the book to inoculate young people not only against the atheistic poison of Dawkins and Co. but also against the theological and scientific confusions of theistic evolutionists (like Ken Miller and Francis Collins). If this book does its job, both these camps will lose much of their traction with young people.

In case that's not enough to convince you to buy the book, Dembski includes the endorsements in his posting. Here's the one that will certainly make you sit up and take notice. With an endorsement like this you will know exactly how much credibility to assign to Understanding Intelligent Design.

“In my book Godless, I showed that Darwinism is the hoax of the century and, consequently, the core of the religion of liberalism. Like John the Baptist, Darwin foretold one of the key tenets of the left’s worldview: that humans are accidental descendants of earthworms, not the unique creations of an all-powerful God. Liberals respond to critics of their religion like Cotton Mather to Salem’s “witches.” With this book, two more witches present themselves for burning: Sean McDowell, whose gift is communicating with young people, and Bill Dembski, often called the Isaac Newton of Intelligent Design. I think Dembski is more like the Dick Butkus of Intelligent Design. His record for tackling Darwiniacs is unmatched. This book gives young people all the ammo they need to take on Darwinism and understand the only viable scientific alternative to Darwinism: Intelligent Design. Every high school student in America needs a copy of Understanding Intelligent Design.”

–Ann Coulter, BESTSELLING author of Godless: The Church of Liberalism

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1. Some of my colleagues won't link to creationist web sites. I disagree with that policy. I think you should visit those sites often. They are the best possible advertisement against Intelligent Design.

Happy Canada Day

 


HAPPY

CANADA

DAY

Canada's official birthday is today. Lot's of people, including me, took yesterday off as well, making it a four-day weekend. Canada is 141 years old.

Here's a photograph of Canada's Fathers of Confederation (there were no mothers) at the Quebec Conference in 1864. I doubt that the average Canadian could name even one of these men. Try it without peeking at the website. Did you get more than five?

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Monday's Molecule #78

 
Today is Tuesday so, once again, it's time for Monday's Molecule.¹

This time there are two molecules and you have to get them both right in order to win. We'll need complete and accurate common names and IUPAC names. The two molecules have something in common, they belong to the same class of compounds. Can you guess what class it is?

As always, there's a connection between today's molecule and a Nobel Prize. The prize was awarded for being the first scientist to recognize that these molecules exist in nature and play an important role in biology. The structure of the molecules was not known when the Nobel Prize was awarded.

The first person to correctly identify the molecules and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.

THEME:

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

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

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

UPDATE: This week's winner is Neel Patel. Here's his answer ..

Both molecules are fat-soluble vitamins.

The first molecule is Vitamin D3, or cholecalciferol. The IUPAC name is (3â,5Z,7E)-9,10-secocholesta-5,7,10(19)-trien-3-ol.

The second is Vitamin A, or retinol. The IUPAC name is (2E,4E,6E,8E) -3,7-dimethyl-9- (2,6,6-trimethylcyclohex-1-enyl) -nona-2,4,6,8-tetraen-1-ol

The Nobel Prize in Physiology or Medicine in 1929 pertinent to the above two molecules was awarded to Sir Frederick Gowland Hopkins, who was the first to propose the existence of vitamins, which he termed "accessory factors".

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1. I took a day off from posting, just because I was lazy and it was a holiday.

Good Science Writers: Helena Curtis

 
Helena Curtis is another science writer who didn't make it into The Oxford Book of Modern Science Writing. She died in 2005. One of many obituaries appeared in The villager [Helena Curtis, 81, wrote ‘elegant’ science textbooks].

Helena Curtis, a noted science writer and college biology textbook author, died on Feb. 11 at the age of 81. She was a resident of Sag Harbor and Greenwich Village.

Her first book, “The Viruses,” published in 1965 by Natural History Press, was followed in 1968 by “The Marvelous Animals.” In 1966, she was signed to a contract for a college biology textbook by Worth Publishers. The idea of a textbook written not by an academic, but by a professional science writer, in consultation with biology experts, was at that time revolutionary and greeted with skepticism. However, when Curtis’s “Biology” was published in 1968, it received a laudatory review in Scientific American by Nobel Laureate Salvador Luria. Through five editions in English it has sold 1.3 million copies. A shorter book, “Invitation to Biology,” has sold 600,000 copies. Both books have enjoyed success in Spanish and Italian editions, with more than 1 million of the books sold in Italian. On the later editions of both books, she was joined by N. Sue Barnes as co-author. Curtis also co-authored “Biology of Plants.”

Curtis’s books and her articles for encyclopedias, journals and magazines were praised for their scientific accuracy, elegant writing and wit. In 1988, Professor John O. Corliss of the University of Maryland said, with regard to the fifth edition of “Biology”: “The writing is about the closest to poetry that a scientific textbook can ever hope to get. It is thoroughly enjoyable, stimulating, imaginative, yet beautifully factual.”

The passage I've chosen is from her biology book. It's the opening paragraphs of Chapter 1. Her phrase "You and I are flesh and blood, but we are also stardust" is one of the most widely quoted sentences ever to come from a biology textbook.

Our universe began, according to current theory, with an explosion that filled all space, with every particle of matter hurled away from every other particle. The temperature at the time of the explosion—some 10 to 20 billion years ago—was about 100,000000000 degrees Celsius (10¹¹ °C). At this temperature, not even atoms could hold together; all matter was in the form of subatomic, elementary particles. Moving at enormous velocities, even those particles had fleeting lives. Colliding with great force, they annihilated one another, creating new particles and releasing great energy.

As the universe cooled, two types of stable particles, previously present only in relatively small amounts, began to assemble. (By this time, several hundred thousand years after the "big bang" is believed to have taken place, the temperature had dropped to a mere 2500°C, about the temperature of white-hot wire in an incandescent light bulb.) These particles—protons and neutrons—are very heavy as subatomic particles go. Held together by forces that are still incompletely understood, they formed the central cores, or nuclei, of atoms. These nuclei, with their positively charged protons, attracted small, light, negatively charged particles—electrons—which moved rapidly around them. Thus, atoms came into being.

It is from these atoms—blown apart, formed, and re-formed over the course of several billion years—that all the stars and planets of our universe are formed, including our particular star and planet. And it is from the atoms present on this planet that living systems assembled themselves and evolved. Each atom in our own bodies had its origin in that enormous explosion 10 to 20 billion years ago. You and I are flesh and blood, but we are also stardust.

This text begins where life begins, with the atom. At first, the universe aside, it might appear that lifeless atoms have little to do with biology. Bear with us, however. A closer look reveals that the activities we associate with being alive depend on combinations and exchanges between atoms, and the force that binds the electron to the atomic nucleus stores the energy that powers living systems.

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Darwinism at the ROM

 
Yesterday I attended a symposium on evolution at the Royal Ontario Museum [Darwin Symposium at the ROM]. The emphasis was on Charles Darwin, in line with the Darwin exhibit that is currently running at the ROM.

What I was expecting was a series of lectures that explain how Darwin fits into modern ideas of evolutionary biology. What I got was an adaptationist lovefest.

This was a free public symposium. By the time it started every seat in the auditorium was full and people were standing at the back. There were about 320 people of all ages and all walks of life. I sat beside a high school teacher and talked to retirees from the suburbs.

The first speaker was Michael Ruse. The original title of his talk was Has Darwinism Expired? but he modified it slightly to Is Darwin's Theory Past Its "Sell By" Date. His opening remarks were promising because he mentioned Stephen Jay Gould and Gould's criticism of Darwinism. He said that this was a distorted picture of evolution. It was downhill from that point on.

Ruse never explained why modern evolutionary theory differs from Darwin's evolution by natural selection. Instead he spent close to an hour going over examples of "evolution by natural selection." Most of his examples were, indeed, evidence of evolution but they were not necessarily evidence of evolution by natural selection. It's clear that Micheal Ruse does not distinguish between "evolution" and "natural selection." Evidence for evolution is treated as evidence for natural selection.

By the time he finished, the audience was completely unaware of random genetic drift, or any other mechanism of evolution. Ruse never explained why anyone would even bother to ask the question he asks in the title of his talk. According to Ruse, Darwinism is still the dominant paradigm in evolutionary biology. When examining characteristics of organisms biologists always ask "What is it for?", according to Michale Ruse. The answer will be explained by natural selection. This is the adaptationist fallacy. The correct question should be "Is this "for" anything?"

I know that Ruse is more of an adaptationist than a pluralist. I know that he favors Richard Dawkins and Daniel Dennett over Stephen Jay Gould and the pluralists. That's not the problem. What bothers me most is that when giving a public lecture Ruse does not even present the other side of the issue. What would it have cost him to mention that there are many evolutionary biologists who do not think of themselves as Darwinists? Why couldn't he explain that many of us think random genetic drift—and not natural selection—is the dominant mechanism of evolution? It doesn't diminish the importance of natural selection and adaptation. It doesn't diminish the contribution of Charles Darwin who still remains the greatest scientist who ever lived.

The second talk was by Spencer Barrett of the Department of Ecology & Evolutionary Biology here at the university of Toronto. Spencer Barrett was recently appointed to the rank of University Professor, our highest rank, in recognition of his work on evolution in flowering plants.

The title of his talk was A Darwinian Perspective on the Evolution of Plant Sexual Diversity and that's an accurate reflection of its content. Spencer Barrett is an adaptationist but in terms of his research he's a very successful example of this wordview. He chooses examples from plant evolution that almost certainly are adaptive and can be explained by natural selection. When faced with a strange example of plant sexual organs, Barrett begins by asking "What is the adaptive significance?"

After lunch we were treated to a lecture by Peter and Rosemary Grant on the evolution of Darwin's Finches. Most of you know the story. The Grants have spent 30 years collecting data on finches in the Galapagos. Everything about the evolution of Darwin's finches is explained by natural selection, especially changes in beak size. It has become the dominant example of evolution by natural selection.

The last lecture was delivered by Allan Baker of the Royal Ontario Museum. his title was Modern Darwinism: Natural Selection and Molecular Evolution. Baker works on bird evolution at the molecular level. He is trying to sort out the complicated, and controversial, relationship of bird clades. Baker pointed out that there are many conflicting data sets in the field and he explained how the use of signature sequences—in his case retrotransposon insertions—can be helpful. He noted in passing that he disagrees with the recent Science paper and cautions that bird evolution is still very much up in the air.

The irony here is that Baker was not studying "Darwinian" evolution at all. In spite of his title, it's extremely unlikely that the changes he looks at are due to natural selection. This was another missed opportunity, in my opinion. Baker could have explained to this public audience that molecular evolution is not Darwinian. It is an example of random genetic drift, which, incidentally, is why there's a molecular clock.

In talking to the lecturers afterward, I tried to find out how they thought about evolution. Baker, is well aware of the importance of random genetic drift. Barrett does not agree with me when I say that random genetic drift is the dominant mechanism of evolution at the molecular level and he does not agree that drift plays a role in speciation. Professor Barrett is one of the lecturers in our first year biology course on ecology and evolution. I've pointed out previously that in my second year course the students do not understand or appreciate random genetic drift and they tell me that it is barely mentioned in first year [Freedom in the Classroom]. I really enjoyed talking to Spencer Barrett and I hope we can continue the debate at another time.

The Grants claim that their evidence for natural selection is strong enough to rule out random genetic drift during the years when most of the finch population dies of starvation. The fluctuations in between could be due to drift.

Further reading ...

What Is Darwinism?
A Confused Philosopher
Darwin and Design by Michael Ruse
Why I'm Not a Darwinist
Evolution by Accident
Random Genetic Drift
Visible Mutations and Evolution by Natural Selection
Adaptationomics
Dennett on Adaptationism
The Evolution Poll of Sandwalk Readers

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The Globe and Mail Reviews "Expelled"

 
So far, all of the Canadian reviews of Expelled have been good (i.e., they pan the movie). Some are more creative than others. Liam Lacy's review in the Globe and Mail is one of the best. It's set in the form of ten biblical verses [Expelled: No Intelligence Allowed]. The last verse is,

10. Then the Lord looked upon Ben Stein's work and declared: “Though I am a loving God, quite frankly, Ben, this film is an appallingly unscrupulous example of hack propaganda and it sucketh mightily. What's more, I didn't laugh once.”

The rating is "0." Denyse is going to be so disappointed in her journalist friends.

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Mars to Sequence Cocoa Genome

 
Jonathan Eisen is excited because the Mars company is planning to sequence the cocoa genome [Combining two of my favorite things - chocolate and genomes]. See why this turns him on and why it isn't an example of science by press release.

The original press report is in the Washington Post [Unwrapping the Chocolate Genome]. The relevant point is the following ...

Mars plans to make the research results free and accessible through the Public Intellectual Property Resource for Agriculture, a group that supports agricultural innovation, as they become available. The intent is to prevent opportunists from patenting the plant's key genes.

Kudos to Mars if this turns out to be true.

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In the interest of full disclosure I reveal that one of my children (Jane) works for Mars.

Good Science Writers: David Suzuki

 
Of all the scientist writers who didn't make it into The Oxford Book of Modern Science Writing, David Suzuki surely counts as the most famous rejected Canadian.

David Takayoshi Suzuki earned his Ph.D. from the University of Chicago in 1961 and was a Professor at the University of British Columbia from 1963 until he retired in 2001. His research interests centered on the genetics of Drosophila melanogaster.

Suzuki founded the radio program Quirks and Quarks and serves as the host of the TV program On the Nature of Things. He has written 43 books and has received numerous awards for his contributions to science education. For the past three decades Suzuki has concentrated his efforts on environmental issues. Whether you agree with him or not, he is one of the world's best science writers.

The David Suzuki Foundation was set up, "to find ways for society to live in balance with the natural world that sustains us. Focusing on four program areas – oceans and sustainable fishing, climate change and clean energy, sustainability, and the Nature Challenge - the Foundation uses science and education to promote solutions that conserve nature and help achieve sustainability within a generation."

This essay on The Beauty of Wind Farms is copied from the New Scientist website. It was published on April 16, 2005.

OFF the coast of British Columbia in Canada is an island called Quadra, where I have a cabin that is as close to my heart as you can imagine. From my porch on a good day you can see clear across the waters of Georgia Strait to the snowy peaks of the rugged Coast Mountains. It is one of the most beautiful views I have seen. And I would gladly share it with a wind farm.

But sometimes it seems like I'm in the minority. All across Europe and North America, environmentalists are locking horns with the wind industry over the location of wind farms. In Alberta, one group is opposing a planned wind farm near Cypress Hills Provincial Park, claiming it would destroy views of the park and disturb some of the last remaining native prairie in the province. In the UK more than 100 national and local groups, led by some of the country's most prominent environmentalists, have argued that wind power is inefficient, destroys the ambience of the countryside and makes little difference to carbon emissions. And in the US, the Cape Wind Project, which would site 130 wind turbines off the coast of affluent Cape Cod, Massachusetts, has come under fire from famous liberals, including Senator Edward Kennedy and Walter Cronkite.

It is time for some perspective. With the growing urgency of climate change, we cannot have it both ways. We cannot shout from the rooftops about the dangers of global warming and then turn around and shout even louder about the "dangers" of windmills. Climate change is one of the greatest challenges humanity will face this century. It cannot be solved through good intentions. It will take a radical change in the way we produce and consume energy - another industrial revolution, this time for clean energy, conservation and efficiency.

We have undergone such transformations before and we can do it again. But first we must accept that all forms of energy have associated costs. Fossil fuels are limited in quantity and create vast amounts of pollution. Large-scale hydroelectric power floods valleys and destroys animal habitat. Nuclear power is terribly expensive and creates radioactive waste.

Wind power also has its downsides. It is highly visible and can kill birds. The fact is, though, that any man-made structure can kill birds - houses, radio towers, skyscrapers. In Toronto alone, it is estimated that 10,000 birds collide with the city's tallest buildings every year. Compared with this, the risk to birds from well-sited wind farms is very low.

Even at Altamont Pass in California, where 7000 turbines were erected on a migratory route, only 0.2 birds per turbine per year have been killed. Indeed, the real risk to birds comes not from windmills but from a changing climate, which threatens the very existence of bird species and their habitats. This is not to say that wind farms should be allowed to spring up anywhere. They should always be subject to environmental impact assessments. But a blanket "not in my backyard" approach is hypocritical and counterproductive.

Pursuing wind power as part of our move towards clean energy makes sense. It is the fastest-growing source of energy in the world - a $6 billion industry last year. Its cost has dropped dramatically over the past two decades because of larger turbines and greater knowledge of how to build, install and operate turbines more effectively. Prices will likely decrease further as the technology improves.

Are windmills ugly? I remember when Mostafa Tolba, executive director of the United Nations Environment Programme from 1976 to 1992, told me how when he was growing up in Egypt, smokestacks belching out smoke were considered signs of progress. Even as an adult concerned about pollution, it took him a long time to get over the instinctive pride he felt when he saw a tower pouring out clouds of smoke.

We see beauty through filters shaped by our values and beliefs. Some people think wind turbines are ugly. I think smokestacks, smog, acid rain, coal-fired power plants and climate change are ugly. I think windmills are beautiful. They harness the power of the wind to supply us with heat and light. They provide local jobs. They help clean our air and reduce climate change.

And if one day I look out from my cabin's porch and see a row of windmills spinning in the distance, I won't curse them. I will praise them. It will mean we are finally getting somewhere.

Today I was reminded of David Suzuki when John Pieret quoted from an article that Suzuki just published on cnews.canoe.ca [What a difference 50 years makes]. Here's an excerpt ...

I began speaking out on television in 1962 because I was shocked by the lack of understanding of science at a time when science as applied by industry, medicine, and the military was having such a profound impact on our lives. I felt we needed more scientific understanding if we were to make informed decisions about the forces shaping our lives. Today, thanks to computers and the Internet, and television, radio, and print media, we have access to more information than humanity has ever had. To my surprise, this access has not equipped us to make better decisions about such matters as climate change, peak oil, marine depletion, species extinction, and global pollution. That's largely because we now have access to so much information that we can find support for any prejudice or opinion.

Don't want to believe in evolution? No problem - you can find support for intelligent design and creationism in magazines, on websites, and in all kinds of books written by people with PhDs. Want to believe aliens came to Earth and abducted people? It's easy to find theories about how governments have covered up information on extraterrestrial aliens. Think human-induced climate change is junk science? Well, if you choose to read only certain national newspapers and magazines and listen only to certain popular commentators on television or radio, you'll never have to change your mind. And so it goes. The challenge today is that there is a huge volume of information out there, much of it biased or deliberately distorted. As I think about my grandson, his hopes and dreams and the immense issues my generation has bequeathed him, I realize what he and all young people need most are the tools of skepticism, critical thinking, the ability to assess the credibility of sources, and the humility to realize we all possess beliefs and values that must constantly be reexamined. With those tools, his generation will certainly leave a better world to its children and grandchildren 50 years from now.

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[Photo Credit: Wikipedia: The copyright holder of this file, Joshua Sherurcij, allows anyone to use it for any purpose, provided that the copyright holder is properly attributed. Redistribution, derivative work, commercial use, and all other use is permitted.]

The Oxford Book of Modern Science Writing

 
The Oxford Book of Modern Science Writing, Richard Dawkins ed., Oxford University Press, Oxford, United Kingdom (2008)

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I'd be lying if I said I read this book from cover to cover. Richard Dawkins has collected 83 short examples of science writing. Most of them are quite good, some of them are excellent, and some I didn't finish. The examples span the entire range of traditional science disciplines with a heavy emphasis on physics, astronomy, and biology. There are very few examples from chemistry or geology.

These are selections picked by Richard Dawkins and they strongly reflect his views of science and of good writing. One of the criteria for inclusion is "good writing by professional scientists, not excursions into science by professional writers" (p. xvii). There's nothing wrong with that, as long as Dawkins sticks to his guns.

Unfortunately, there are so many exceptions to the rule that one wonders why the rule was made up in the first place. We don't have anything by Carl Zimmer (a non-scientist), for example, but we do have examples from Matt Ridley who, while he has a Ph.D. in science has never been a professional scientist. Neither has Daniel Dennett. Rachel Carson worked as a biologist for a while but she was a full-time writer by the time she wrote most of her books. Roger Lewin has never been a professional scientist, as far as I know.

Perhaps Dawkins meant to restrict his authors to those who have earned an advanced degree in science regardless or whether they actually became working scientists. Perhaps that's what he means by "professional scientist." If that's what he means then, as he points out on page 171, Margaret Thatcher might qualify since she got her Master's degree in Chemistry and worked with with Dorothy Hodgkin as an undergraduate. Hodgkin is included. Thatcher isn't.

Dawkins has three other rules. First, all of the works were produced within the past 100 years. This is an excellent restriction, in my opinion. Second, the works must have been first published in English—no translations are allowed (with a few exceptions). Finally, no works by Richard Dawkins are included.

Dawkins introduces each author with a few paragraphs of background material that often includes personal anecdotes. This is where we learn that Dawkins and Gould, "enjoyed—or suffered—a kind of love/hate relationship." We also discover that Fred Hoyle wrote an article that serves as, "an example of the insight that a physical scientist can bring to biology," bearing in mind that it was written, "before Hoyle began the perverse campaign of his old age, against all aspects of Darwinism."¹

Some of the choices are very pleasant surprises. I had never heard of James Jeans, the first author in the book. His entry is so interesting—and so in line with modern thought—that I can't resist a quotation. Keep in mind that this was written in 1930.

Into such a universe we have stumbled, if not exactly by mistake, at least as the result of what may properly described as an accident. The use of such a word need not imply any surprise that our earth exists, for accidents will happen, and if the universe goes on for long enough, every conceivable accident is likely to happen in time.

Many of Dawkins' choices have nothing to do with biology but, of those that do, most extol the virtues of design and natural selection. For example, there is a passage from Helena Cronin's The Ant and the Peacock that's as fine an example of science-related prose as can be found anywhere in the anthology. It is good writing but I don't it is good science. Dawkins does, and it's his book and his choice.

This brings me to an important point. In order to be included in any collection of good science writing the work has to be both good writing and good science.² Both of these criteria are subjective so whether an author is included or not will depend very much on the point of view of the editor. In this case we learn almost as much about Richard Dawkins as we do about the authors he selects.

And the authors he omits. Of the three giants of population genetics, R.A. Fisher and J.B.S. Haldane get included but Sewell Wright isn't even named. There's nothing by Richard Lewontin, Niles Eldredge, Gabriel Dover or David Raup. Ken Miller, Francis Collins, and Simon Conway-Morris are missing as well. Daniel Dennett is there but not Michael Ruse. One gets the impression that a similar book edited by Stephen Jay Gould would look quite different.

Now don't get me wrong. There's nothing wrong with this. As far as I'm concerned "good" science writing includes scientific accuracy and Dawkins has every right to pick and choose those authors who get it right, in his opinion. However, I'd prefer that editors lay their cards on the table and admit openly that their selections are influenced by this bias.³

No book of this sort should be complete without Peter Medawar and this book is no exception. Medawar's famous wit is unequaled, and often unappreciated. I fear it is a lost art. Dawkins is such a fan of Medawar (as am I) that he includes five excerpts from his books and essays—more than any other science writer.

Let me close with a quotation from Peter Medawar's essay on Science and Literature where Medawar is discussing a modern trend among philosophers and scientists to write very complicated prose,

Let me end this section with a declaration of my own. In all territories of thought which science or philosophy can lay claim to, including those upon which literature also has a proper claim, no one who has something original or important to say will willingly run the risk of being misunderstood: people who write obscurely are either unskilled in writing or up to some mischief. The writers I am speaking of are, however, in a purely literary sense, extremely skilled.

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1. In contrast to Dawkins' praise, I found the passage from Hoyle to be almost incomprehensible. It is not good science writing, in my opinion, and it certainly isn't "insightful."

2. There are exceptions. Dawkins included a passage from R.A. Fisher's book The Genetical Theory of Natural Selection even though he (Dawkins) recognizes that it may not be an example of good writing.

3. I'm going to post some examples of my own biases with respect to good science writing, concentrating almost exclusively on those writers that don't appear in The Oxford Book of Modern Science Writing.

Nobel Laureate: Susumu Tonegawa

 

The Nobel Prize in Physiology or Medicine 1987.

"for his discovery of the genetic principle for generation of antibody diversity"

Susumu Tonegawa (1939 - ) received the Nobel Prize in Physiology or Medicine for working out the mechanism of generating antibody diversity. This was one of the fundamental problems in immunology—and, indeed, all of biology. How do antibodies recognize so many different antigens?

We now know the answer thanks to Tonegawa and his coworkers. The genes for antibody proteins are constructed in antibody-producing cells by recombining bits of DNA from several different locations. Millions of different permutations can be constructed to create a random library of antibody molecules. The chance that one of these randomly constructed antibody molecules will recognize a new antigen, such as virus, is very high.

This is one of the most significant Nobel Prizes of the 2oth century. Tonegawa's discovery deserves a lot more attention that it normally gets.

The presentation speech was delivered (in Swedish) by Professor Hans Wigzell of the Karolinska Institute.

THEME:
Nobel Laureates

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

The defence of our body against infections is carried out by the immune system, a talented cellular society with a capacity to distinguish between self and non-self and with a memory capable of remembering a previous contact for decades. The system is managing this through the inbuilt capacity in a single human being to produce billions of different forms of protective molecules, antibodies. The Nobel Prize of this year is given for the elucidation of the unique capacity of the immune system to produce this enormous diversity of specific antibodies.

Susumu Tonegawa is the great molecular biologist in immunology. In a series of ingenious experiments carried out in the middle of the 1970's he solved the problem how our limited genetic material is capable of generating the diversity required to create protection against established as well as future disease provoking microorganisms. When Tonegawa did his experiments at the Basel Institute of Immunology in Switzerland other scientists had already generated a-considerable amount of knowledge regarding the features and functions of antibodies. But this knowledge had also led to uncertainty and even confusion. Antibodies are proteins and their structure is strictly ruled by genes, by the DNA in our chromosomes. When Tonegawa carried out his experiments it was commonly believed that each protein, each polypetide chain, was governed by its gene in a relation one to one. But at the same time calculations on the number of genes in the chromosomes in man determining proteins gave a number probably below one hundred thousand genes. They should suffice to all the proteins in the body, to the hemoglobin in the red blood cells, to the pigment in our eyes and so on. Only a minor part, maybe one percent, could probably be used for the creation of antibodies. Around one thousand genes being able to create billions of different forms of antibodies? The equation seemed impossible to solve.

Our antibodies are made up of two sorts of polypeptide chains, short and long ones. Tonegawa did first acquire a toolbox, filling it with the best precision tools there were of hybrid-DNA nature, developed new methods and started to study the actual construction of the genes determining the short chains of antibody molecules. He discovered something entirely new and revolutionary in genetics. On the chromosome where the gene for the short chain was expected to be located, there was not one single, but a string, of pearls of genes. One special gene resided at one position whereas two other sets of variable genes create two gene families, in all maybe around one hundred genes. When a cell should start to make antibodies - this was preceded by a gene-lottery.

One member of the largest gene family selected at random was cut out from the chromosome and moved close to a member of the second gene family, whereafter they created a functional gene for the short chain together with the solitary gene. Three and not one gene participate in the creation of the short chain of antibody molecules. Each member in one family can probably be linked to any one of the members of the second gene family, increasing variability by multiplication. The results showed beyond doubt that our body has the capacity to carry out advanced recombinant DNA processes. The intelligence of Nature can also be seen as the studies went on. The recombination of genes and their coupling together do not occur in exactly the correct manner. While such relative misfits should in other systems be bad, here they constituted yet another mechanism of increasing the diversity of antibodies. Experiments by Tonegawa as well as other scientists also revealed that the same genetic lottery principle did apply to the generation of the long chain although here the number of variants were even larger. Four different genes could be shown to create these chains together. The number of variant short chains should then be multiplied by the combinatorial possibilities of the heavy chain to give the variation at the antibody level, a fact which will also drastically enhance the diversity of antibodies.

The equation was in essence solved. A few hundred genes are used by the body in a new, revolutionary way and can thus generate billions of different antibodies. Through this genetic lottery the immune system is always prepared to react against known as well as unknown microorganisms. The economic usage of precious DNA is compensated by wasting more dispensable material. Every minute our body produces several millions of white blood cells - lymphocytes. Each one of these has undergone the hybrid-DNA procedure and is prepared with its own, unique antibodies. If not called upon to react they will rapidly die. If, however, they make contact with the fitting foreign structures they receive a reward, i.e., they are allowed to proliferate and live longer. After the great randomized gene lottery natural selection will pick the winners, thereby generating specific immunity, the cheapest and most efficient protection there is against infections.

Dr. Tonegawa,

On behalf of the Nobel Assembly of the Karolinska Institute I would like to congratulate you on your outstanding accomplishments and ask you to receive the Nobel Prize in Physiology or Medicine from the hands of His Majesty the King.

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[Photo Credit: Nature]

[Figure credit: The figure showing immunoglobulin gene rearrangment is from carthage.org]

Tangled Bank #108

 
The latest issue of Tangled Bank is #108. It's hosted at Wheat-dogg's world [The Tangled Bank #108].

Welcome to The Tangled Bank 108 and to the little-known but still fascinating Wheat-dogg’s World. I hope that after you peruse the fine entries in this edition of The Tangled Bank you’ll stroll around and check out things here in my neck of the Worldwide Woods.

Today we have science bloggers musing on some of the greater profundities of the universe as well on more concrete issues closer to home. Some of these posts ask more questions than they answer, but heck that’s what science is all about, hey?

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

Get a Job at CFI

 
The Center for Inquiry (Toronto) is looking for someone to help out with their various activities. This is a part-time job. It's a wonderful opportunity for a student.

CFI ONTARIO IS HIRING A LONG-TERM PART-TIME
CENTRE & FIELD ORGANIZER!

Please spread the word to anyone interested in taking on a decisive leadership position in the expanding freethought movement in Canada. Position starts mid July.

Deadline to apply: Monday, July 7.
Full info and updates will be provided online.
Visit Center for Inquiry.

The Centre for Inquiry is an international education and outreach organization dedicated to promoting and advancing reason, science, secular ethics and freedom of inquiry in all areas of human endeavour. We engage in educational lectures, debates and conferences, coordinate 30 campus freethought groups across Canada, run a robust series of secular humanist social and community services, and undertake advocacy defending church-state separation, the integrity of science and equality rights for non-believers. The new CFI Ontario is CFI's first location in Canada and our nation’s premiere venue for secular humanists, skeptics and freethinkers.

RESPONSIBILITIES:

This position is two-fold:

1. The successful candidate will act as an assistant director at CFI Canada headquarters in Toronto. He/she will lead CFI Ontario’s in-house and ongoing programming, event planning and hosting, promotions, newsletter publishing, social services, campus outreach and membership committees. There will be numerous leadership opportunities through support staff and volunteer recruitment, training, supervision and delegation.
2. CFI's Canadian operations have recently expanded with the launching of new Communities in Montreal and Calgary and the anticipated launch of a Community of Vancouver in the next few months. The successful candidate will provide organizing assistance to our new CFI Communities in Canada.

HOW TO APPLY

If you are interested in applying, please email a cover letter, resume/CV and writing sample as a text, Word or PDF attachment, to Justin Trottier at jtrottier@centerforinquiry.net. Include a brief statement of your academic background, interests, your activities with the skeptic or humanist movements and/or other extracurricular, community, work or voluntary experience of relevance, and why interning at CFI is something you want to do. You are also encouraged to include any documentation or samples of your relevant experiences (eg. media coverage of your event, political policy statement you wrote, poster you created, etc).

This is an exciting opportunity to contribute to the overall growth of the secular community in Canada and to strengthen your relationship with CFI. We hope you will consider joining us.

Position starts mid July. Deadline to apply: Monday, July 7

TIMING/DURATION:

This position will last one year with the possibility of renewal. The daily and weekly time commitment are flexible but would work out to ~ 15-20 hours/week. Please indicate your daily and weekly availability as well as the duration of your commitment.

JOB REQUIREMENTS:

An understanding of the freethought/humanist/skeptic community and/or some demonstration of commitment to the values of free and critical inquiry is essential.

To perform this job successfully an individual must possess excellent skills in organization, promoting and leading. The individual must also have the ability to exercise independent judgment and manage multiple priorities, the ability to organize and lead volunteers, strong verbal and written communication skills, and the ability to represent CFI via public speaking and media appearances. The job frequently involves speaking in front of crowds and other PR activities for which the successful candidate must be comfortable, experienced and proficient. Knowledge of the non-profit sector and community development strategies is ideal.

Since there is some travel access to own car is very helpful. In addition, because the computer resources at CFI Ontario are limited, access to own laptop is also ideal.

Since the successful candidate will be involved in setting up our Community of Montreal, he/she must be very comfortable conversing and writing in the French language. In addition, some knowledge of Montreal and Quebec culture is ideal.

ADDITIONAL TECHNICAL KNOWLEDGE

To assist in specific projects, the following technical background is helpful, though not completely required. Candidates without such background should still apply. Candidates with such technical knowledge should highlight it in application:

• Web development experience
• Basic image editing skills in Adobe Photoshop or similar program
• Experience using and maintaining SQL databases (eg. MySQL) or similar technology
• Basic understanding of video technology and video editing, uploading and embedding (e.g. through youtube or google video)
• Proficiency in Adobe Illustrator, Photoshop, Microsoft Publisher or similar program for poster and ad creation

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Selfish Genes

 
In honey bee colonies the queen is the only fertile female. She lays all the eggs. The worker bees are female but sterile. The process of ovulation in worker bees is suppressed in response to phermomes. This is an example of genetic altruism where the reproductive benefit of worker bees is suppressed in favor of the good of the hive. There are good theories about why this would ultimately benefit the workers.

In some hives, a few worker bees can lay eggs and these eggs will hatch. The presence of "cheaters" in an altruistic society is expected and normal. Oxley et al. (2008) looked at the DNA from these "cheater" hives and compared it to the DNA from bees that were sterile. The idea was to identify the gene responsible for suppressing ovulation in workers; presumably that gene was somehow different in the hives with "cheaters."

Here's the abstract of the paper.

The all-female worker caste of the honey bee (Apis mellifera) is effectively barren in that workers refrain from laying eggs in the presence of a fecund queen. The mechanism by which workers switch off their ovaries in queenright colonies is pheromonally cued, but there is genetically-based variation among individuals: some workers have high thresholds for ovary activation, while for others the response threshold is lower. Genetic variation for threshold response by workers to ovary-suppressing cues is most evident in "anarchist" colonies in which mutant patrilines have a proportion of workers that activate their ovaries and lay eggs, despite the presence of a queen. In this study we use a selected anarchist line to create a backcross queenright colony that segregated for high and low levels of ovary activation. We used 191 informative microsatellite loci, covering all 16 linkage groups to identify QTLs for ovary activation and test the hypothesis that anarchy is recessively inherited. We reject this hypothesis, but identify four QTLs that together explain approximately 25% of the phenotypic variance for ovary activation in our mapping population. They provide the first molecular evidence for the existence of quantitative loci that influence selfish cheating behavior in a social animal.

This is an interesting paper but that's not the reason for this posting. The real reason is to contrast the actual paper with the press release from the University of Western Ontario (Canada) [Discovery proves 'selfish gene' exists]. Here's the complete press release.

A new discovery by a scientist from The University of Western Ontario provides conclusive evidence to support decades-old evolutionary beliefs about the existence of a so-called selfish gene.

Since renowned British biologist Richard Dawkins ("The God Delusion") introduced the concept of the ‘selfish gene’ in 1976, scientists the world over have hailed the theory as a natural extension to the work of Charles Darwin.

In studying genomes, the word ‘selfish’ does not refer to self-centred behaviour but rather to the blind tendency of genes wanting to continue their existence into the next generation. Ironically, this ‘selfish’ tendency can appear anything but selfish when the gene does move ahead for selfless and even self-sacrificing reasons.

For instance, in the honey bee colony, a complex social breeding system described as a ‘super-organism,’ female worker bees are sterile. The adult queen bee, selected and developed by worker bees, is left to mate with male drones.

Because the ‘selfish’ gene controlling worker sterility has never been isolated by scientists, the understanding of how reproductive altruism can evolve has been entirely theoretical – until now.

Working with Peter Oxley of the University of Sydney in Australia, Western biology professor Graham Thompson has, for the first time, isolated a region on the honey bee genome that houses this ‘selfish’ gene in female workers bees.

“We don’t know exactly which gene it is, but we’re getting close.”

“This basically provides a validation for a huge body of socio-biology,” says Thompson, who adds the completion of Honey Bee Genome Project in 2006 was crucial to this discovery.

So, what's the beef? The problem is that the press release is horribly confusing. In The Selfish Gene Dawkins argues that one can look at evolution from the perspective of the gene and not the organism. The goal of each and every gene, according to Dawkins, is to replicate itself and pass on copies to future generations. Every gene (allele) is selfish in his view. The selfish gene of The Selfish Gene has nothing to do with altruism. At least not directly.

Now, according to the Dawkins' view of evolution, worker sterility is not a violation of the selfish gene principle. Dawkins believes that Hamilton is correct and that altruistic behavior can be explained as an indirect way of propagating one's genes to future generations. Thus, the bee gene is a selfish gene in the Dawkins sense, but so is every other gene (allele) in the bee genome.

This study is not "conclusive evidence" of selfish genes. We've had that kind of conclusive evidence ever since the discovery of alleles that confer fitness advantage—alleles such as those for antibiotic resistance gene in bacteria. This study is interesting because it points to the discovery of altruistic genes (alleles) but that something quite different from what it says in the press release. The "cheater" allele represents selfishness of a different kind.

Incidentally, there's nothing in paper itself about "selfish genes" or Richard Dawkins.

If you want to follow up on this topic you should read the comments on Richard Dawkins.net [New discovery proves 'selfish gene' exists]. As you might imagine, the readers over there are split between those who hail this as confirmation that Dawkins is vindicated and those who have actually read The Selfish Gene. Many are calling for clarification from Richard Dawkins himself. I hope he responds because this is a perfect opportunity for him to set the record straight.

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[Photo Credit: The Telegraph (UK)]

Oxley, P.R., Thompson, G.J., Oldroyd, B.P. (2008) Four QTLs that Influence Worker Sterility in the Honey Bee (Apis Mellifera). Genetics. 2008 Jun 18. [Epub ahead of print]Click here to read [PubMed] [DOI: 10.1534/genetics.108.087270]

Monday's Molecule #77

 
Today's molecule is related to a previous Monday's Molecule. This time you have to name the molecule and identify the various symbols on the cartoon. Be as specific as possible.

There's a direct connection between today's molecule and a Nobel Prize. The prize was awarded for figuring out how this molecule was made. It was one of the most brilliant discoveries of the 20th century.

The first person to correctly identify the molecule (and its parts) and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are five ineligible candidates for this week's reward. You know who you are.

THEME:

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

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

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

UPDATE: The molecule is immunoglobulin G (IgG)—same as last week. The V, D, and J symbols stand for variable, diversity, and joining regions of the protein. The antigen binding site is formed from the combination of these regions on the heavy (H) chain and the light (L) chain of the molecule. The ability of antibodies to recognize a huge number of different antigens is due to formation of a huge number of different antigen-binding sites. This is achieved by rearranging the genome in order to bring together one of hundreds of V regions with 20 or so D regions and 5-6 J regions. The recombination events are associated with mutations that serve to create even more diversity.

The generation of antibody diversity by genomic rearrangement was discovered by Susumu Tonegawa who received the Nobel PRize in 1987. Today's winner is Alex Ling or the University of Toronto.

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Peter McKnight Reviews Expelled

 
The movie is called Expelled: No Intelligence Allowed. Perhaps you've heard of it? After flopping in the USA it's about to open in Canada on June 27th. I heard an ad on the radio today as I was driving to work.

The movie is full of errors and lies. For a complete list, check out Expelled Exposed.

Peter McKnight of The Vancouver Sun reviewed the movie last Saturday [No intelligence allowed in Stein's film]. It's an excellent review. I recommend you read the whole thing. Here are the opening paragraphs ...

Although you're probably not aware of it, scientists, lobby groups, the media and the courts are all united in a massive conspiracy to destroy your freedom. But have no fear, freedom fighter Ben Stein is here.

That, in effect, is the thesis of Expelled: No Intelligence Allowed, the new anti-science "documentary" which opens across Canada on June 27, was produced by Vancouver's Premise Media, and stars Stein, the lawyer, actor, game show host and speechwriter for former U.S. president Richard Nixon.

The subtitle of the film is wholly appropriate as there is precious little intelligence displayed in its more than 90 minutes. But the subtitle's reference to the content of the film was unwitting -- it was meant to refer to a giant conspiracy to banish intelligent design theory from the halls of academe and the culture as a whole.

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[Hat Tip: John Pieret]