Sandwalk: May 2009

Sunday, May 31, 2009

Another Blogger Leaves the SEED Blogs (ScienceBlogs.con)

Dr. Joan Bushwell's Chimpanzee Refuge is the latest blog to jump ship. That makes three or four blogs that have left the SEED group in the past few weeks. Most of them have been fairly cryptic about their reasons for leaving but Kevin Beck hints at something sinister happening behind the scenes [Bon(obo) voyage: the chimps are loping away from ScienceBlogs.com].

I also want to be open about what I say without fear of being castigated as a misogynist (a term often used inaccurately - try "sexist," folks), a tremendously ironic notion given that I harbor genuine ovaries (although going dormant) and had some pretty hair-raising experiences during my fairly long scientific career which allow me to speak from a solid platform of experience and credibility.

The latter sniping derives from my stumbling upon some very shoddy behavior in the back rooms of Science Blogs, stuff that removed any doubt that leaving Science Blogs for an independent venue was the thing to do. The majority of the folks that blog here do not participate in this -- uh -- "community" forum, but the ones who do are fairly heavy hitters and like it or not, they set a tone.

Does anyone out there want to explain this? What's going on n the back rooms of ScienceBlogs?

Saturday, May 30, 2009

John Hawks on "Adaptationists vs Pluralists"

John Hawks recently posted a comment about adaptationists [see Richard Lewontin: "[T]oo rapid for genetic adaptation"].

Hawks said ...

I don't really find the "pluralist versus adaptationist" debate very interesting. Despite the vocal complaints of some, I can't ever seem to locate the mythical "adaptationists" who deny that non-adaptive evolution ever happens. So the "debate" always comes down to whether particular adaptive hypotheses are true. Since no scientific hypothesis is true a priori, and since "those adaptationists are always saying stupid things" is not a scientific argument, I don't see the point.

I'm astonished that, after all these years, the adaptationists still don't get it.

First, the mythical adaptationist is a straw man that only exists in the minds of the adaptionists. This particular straw man was easily disposed of in the original Spandrel's paper. It is only resurrected by those who haven't been paying attention

Second, the debate does not come down to "whether adaptive hypotheses are true." It comes down to whether any adaptive hypothesis is true. When speculating on mechanisms, adaptationists tend to ignore any mechanism of evolution other than natural selection That's the problem. As a general rule, they don't seriously consider the possibility that the correct explanation may not be adaptation.

It's a difference in worldviews. Pluralists tend to look at an evolutionary outcome and ask, "What mechanism of evolution caused this?" Adaptationists tend to look at the same outcome and ask, "How can this be explained by natural selection?" Adaptationists know about random genetic drift—they just don't think it's an important player when it comes to the parts of evolution that they're interested in. I think that's a bad assumption.

Friday, May 29, 2009

The Mouse Genome is "Finished"

The first draft of the mouse genome was published by the Mouse Genome Sequencing Consortium back in 2002. At the time it was the only available non-human genome sequence. Since then several dozen other draft sequences have been published and many more are in progress. You can view a complete list at NCBI: Mammalian Genomes.

A finished version of the human genome sequence was published a few years ago and up until this month it was the only one listed as "complete." Now you can add the Mus musculus (mouse) genome to the list of complete publicly available genome sequences (Church et al. 2009).

When scientists say that a genome is complete or "finished" they don't really mean it. What they mean is that the effort has reached the point of diminishing returns. They are confident that they have found almost all of the genes and most of the important bits but they're well aware of the fact that some parts of the genome are missing.

This figure from the Church et al. paper illustrates the extent of a "finished" sequence. The green chromosomes represent the original draft sequence. Unsequenced regions are shown in black. As you can see, there were many gaps in the original sequence—176,000 to be exact.

The blue chromosomes represent the "finished" genome sequence. There are a lot fewer black regions and they are mostly confined to the centromeres/telomeres at the top ends of the chromsomes. As is the case with the human genome, these regions are mostly repetitive DNA that resists assembly into large blocks [The Human Genome Sequence Is not Complete].

The reason why the Y chromosome is missing is because it was a female genome that was sequenced.

Mice have 19 autosomes (non-sex chromosomes, see karyotype above). When you compare the mouse and human genomes you can see right away that the sequences of chromosomes aren't conserved. What is conserved are large blocks of sequence that may be found on one particular mouse chromosome but on a completely different human chromosome.

The mapping of these conserved synteny relationships reveals a great deal about the evolution of human and mouse chromosomes from a common ancestor. For example, the yellow block of sequence at the tip of human chromosome 1 (below) is found on mouse chromosome 4. The other parts of mouse chromosome 4 are found on human chromosome 6, 8, and 9.

What this means is that there are large blocks of genes that have been preserved since the time of the common ancestor. There are 334 chromosomal breakpoints that define the blocks of homologous sequence between human and mouse. The rearrangements took place in both lineages and the frequency of such rearrangements seems to be similar in most mammalian lineages.

The current "build" of the mouse genome has 20,210 protein-encoding genes. This is a substantial reduction from the 22,011 genes predicted in the initial draft sequence. As a general rule, the number of confirmed genes declines with each improvement in the sequence. This is mostly due to the joining together of gene fragments that were misidentified in the first draft. The authors note that 30% of the genes in the "finished" sequence were disrupted by errors and gaps in the first draft. Some new genes are added because of the addition of new sequence data but this doesn't compensate for the genes that are removed.

A total of 2,185 new genes were added. Most of them are duplicates of genes previously identified in the original draft sequence. In fact, the biggest change in the "finished" sequence is the identification of 126,000 Kb (126Mb) of duplicated sequences that were not detected in the first draft. This makes the mouse genome—with about 5% of segmentally duplicaed sequence—similar to the human genome. Initially there were hardly any duplicated regions in the mouse genome leading to speculation that duplications were much more common in primates.

Almost half of the duplicated regions exhibit different copy numbers in various strains of mice. Since the sequenced genome comes from a highly inbred line of laboratory mice (C57BL/6J), it is possible that the o0bserved copy number differs substantially from wild-type mice.

The human genome has 19,042 protein-encoding genes. Of these 15,187 (80%) have clear orthologs in the mouse genome. (Orthologs are homologous genes in the same location. They are related by descent from a common ancestor.) The orthologous genes represent 75% of the mouse genes. Most of the remaining genes are not novel genes but duplicates of the orthologs.

Surprisingly, there were only 12,845 orthologous genes in the first draft sequence. The difference is due to the identification of mistakes in the earlier data where sequence and assembly errors led to the misidentification of conserved genes. What this means is that a substantial number of papers comparing humans and mouse genomes will need to be re-evaluated. Here's how the authors put it ...

The shortcomings of the initial draft assembly are readily apparent now that a more-complete genome assembly is available. Undoubtedly these have led to incomplete or inaccurate understanding of some aspects of mouse biology. The availability of high quality genome sequence for the mouse will lead the way in dismissing some commonly held misconceptions and, more importantly, in revealing many previously hidden secrets of mouse biology.

The total length of protein-encoding exons in the mouse genome is 33,500 Kb (33.5 Mb). The revised genome size is 2,660,000 Kb (2.66 Gb). Thus, protein-encoding regions represent only 1.3% of the genome. This is similar to the value in the human genome (1.1% or 32.6 Mb out of 3.08 Gb).

There are many important non-coding sequences including centromeres, telomeres, origins of replication, scaffold attachment regions etc. All genes have substantial regulatory regions that aren't counted in the 1.3% of the genome that encodes protein. In addition, there are hundreds of tRNA genes, ribosomal RNA genes, and genes for essential small RNAs.

Nevertheless, a substantial proportion of the mouse genome (>90%) appears to be junk DNA with no known function. Most of it (~50%) consist of active and degenerate transposons similar to the LINES and SINES found in all other mammalian genomes.

[Photo Credit: Oak Ridge National Laboratory]

Church, D.M., Goodstadt, L., Hillier, L.W., Zody, M.C., Goldstein, S., et al. (2009) Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse. PLoS Biol 7(5): e1000112. [doi:10.1371/journal.pbio.1000112 ]

Thursday, May 28, 2009

A Nomination Meeting

Last Fall I joined the Liberal Party of Canada in order to have a say in electing a new leader and a new candidate in my riding. My riding is Mississauge-Erindale in the city of Mississauga, just west of Toronto, Ontario, Canada.

The candidate in the last election was Omar Alghabra, who at the time was the sitting member of the House of Commons in Ottawa. He lost the election by 400 votes.

Well, as it turns out, I didn't get a chance to vote for a new leader. The new leader, Michael Ingatieff, was acclaimed when when eveyone else dropped out of the race last December.

I looked forward to a healthy debate on choosing a candidate in my riding.

I received a notice in the mail on May 12th stating that there would be a nomination meeting in two weeks. All nomination forms must be received by the Liberal Party office in Toronto on May 18th at the latest. That left six days, counting Saturday and Sunday, to fill out a raft of forms [Nomination Rules].

The meeting was last night and the only candidate was Omar Alghabra. I took a picture of him on my cell phone at the meeting. I was told by the riding Chair that no other candidates would have been permitted but it was a moot point since the system was set up in such a way that it would have been almost impossible to get another nomination in on time.

This doesn't seem very democratic and it seems inconsistent with the openness that the Liberal Party desires. I don't know if Omar would have been nominated anyway but what I do know is that I would have been a lot happier if there had been some debate and discussion about choosing a person who could win the next election.

I feel that I've been manipulated. I wasn't the only one at the meeting who felt that way.

It's going to be hard to get excited about working for Omar during the upcoming campaign. The whole idea behind openness and democracy is to let everyone have their say. When that happens, people feel they're part of the process and they're willing to work with the system no matter which candidate is chosen to run in a riding. Competition and debate are healthy. Secrecy and manipulation are not.

Nobel Laureate: Willem Einthoven

The Nobel Prize in Physiology or Medicine 1924

"for his discovery of the mechanism of the electrocardiogram"

Willem Einthoven (1860 - 1927) won the Noble Prize in 1924 for discovering a practical machine for detecting the electrical actions of the heart. He discovered the electrocardiogram and identified its characteristic features.

Einthoven's apparatus was based on the string galvanometer, which he had developed a number of years earlier. The importance of an accurate electrocardiogram in diagnosing various heart conditions was instantly recognized. But first, the actions of a normal heart had to be carefully recorded and explained. The explanation put forth by Einthoven proved to be substantially correct.

Here's how the standard electrocardiogram is described in the Presentation Speech.
THEME:
Nobel Laureates

However, in his work in 1908 Einthoven gave an interpretation of the electrocardiogram. He starts from the fact that the stimulus (of the contraction process, the «negativity») is propagated as a wave in the muscular system of the heart. The string of the galvanometer, connected with the heart in a closed circuit in one of the usual ways, remains in the original position not only when the heart is at rest, but also when the «negativity» of the assemblage of points of the heart wall show the same value. A deflection is therefore in the first place to be expected at the beginning and at the end of a systole, and it presupposes that the condition of activity does not occur, respectively cease, simultaneously in all elements of the muscle. Further: if the contraction process (the stimulus) is propagated symmetrically in relation to the points connected to the galvanometer, then no deflection would take place either. Under such circumstances the electrocardiogram must be determined partly by the starting-point of the stimulus to the heart beat, partly by the conduction system within the heart. The point of departure for the normal heart beat has been sufficiently well known since the middle of the 1890's, the bundle of His also since that time, and Tawara's description of the ramification of the conduction system inside the ventricles known since 1906. According to Einthoven the P-peak is an expression of the propagation of the stimulus wave in the muscular system of the auricle. The negativity wave, corresponding to the stimulus wave in the His-Tawara system, is considered too weak by Einthoven to cause any deflection in the galvanometer. The QRS-complex is determined by the propagation of the stimulus wave in the muscular system of the two ventricles, proceeding in unsymmetrical fashion to the points of lead, starting at different moments at the transition of the tree-like ramified Purkinje's fibres into the various parts of the proper muscular system of the heart. When the contraction process has reached its maximum in all the points of the ventricular wall, the string returns to its original position. When the contraction ceases in the various parts at different moments, a T-peak is obtained.

It is unnecessary in this connection to consider the interpretations proposed by other investigators, as Einthoven's concept is the only one which has proved to be tenable. The interpretation that the P-peak belongs to the auricular systole is mainly based on his observation of electrocardiograms in cases of heart block in patients or during vagus stimulation in dogs. With regard to the interpretation of the QRS-complex Einthoven was evidently the first who has clearly recognized the significance of the conduction system in this connection. The train of thought in the interpretation of the T-peak can already be detected in Burdon-Sanderson's previously mentioned work.

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Mixing Science, Religion, and Politics

The first draft of the human genome sequence was announced on June 26, 2000. There was a huge press conference in the East Room of the White House with Craig Venter, President Bill Clinton, and Francis Collins. British Prime Minister Tony Blair appeared via videolink from London.

The event is recounted on pages 2 & 3 of Francis Collins' book The Language of God. It's worth recalling because it reminds Americans of what they can expect if Collins were to become head of NIH.

But the most important part of his speech that most attracted public attention jumped from the scientific perspective to the spiritual. "Today," [Clinton] said, "we are learning the language in which God created life. We are gaining ever more awe for the complexity, the beauty, and the wonder of God's most divine and sacred gift."

Was I, a rigorously trained scientist, taken aback at such a blatantly religious reference by the leader of the free world at a moment such as this? Was I tempted to scowl or look at the floor in embarrassment? No, not at all. In fact I had worked closely with the president's speechwriter in the frantic days just prior to this announcement, and had strongly endorsed the inclusion of this paragraph. When it came time for me to add a few words of my own, I echoed this sentiment: "It's a happy day for the world. It is humbling for me, and awe-inspiring, to realize that we have caught the first glimpse of our own instruction book, previously known only to God."

What was going on here? Why would a president and a scientist, charged with announcing a milestone in biology and medicine, feel compelled to invoke a connection with God? Aren't the scientific and spiritual worldviews antithetical, or shouldn't they at lest avoid appearing in the East Room together? What were the reasons for invoking God in those two speeches? Was this poetry? Hypocrisy? A cynical attempt to curry favor from believers, or to disarm those who might criticize this study of the human genome as reducing humankind to machinery? No. Not for me. Quite the contrary, for me the experience of sequencing the human genome, and uncovering this most remarkable of all texts, was both a stunning scientific achievement and an occasion of worship.

Wednesday, May 27, 2009

Faith and Evolution at the Discovery Institute

The Discovery Institute has a new website called Faith + Evolution. It's designed to explore the relationship, if any, between the Christian faith and science.

Prominently featured on the home page is an article by Jonathan Wells.

Is Francis Collins Right about Evolution?

Francis Collins feels that intelligent design poses a serious problem to Christian belief because it rejects Darwinian evolution, which he feels is supported by overwhelming evidence. But the only evidence Collins cites for Darwin’s mechanism of variation and selection is microevolution—minor changes within existing species. And the principal evidence he cites for Darwin’s claim of common ancestry is DNA sequences that he says have no function—though genome researchers are discovering that many of them do have functions.

Collins’s defense of Darwinian theory turns out to be largely an argument from ignorance that must retreat as we learn more about the genome—in effect, a Darwin of the gaps.

Wells is referring to the evidence of shared pseudogenes and other genomic signatures of common descent. This won't do, according to Wells. Collins is not one of the good guys.

I wonder if Jonathan Wells has read a book called The Edge of Evolution? It was published in 2007. The author is Michael Behe—a Senior Fellow at the Discovery Institute.

Behe also describes the evidence from pseudogenes. Here's an excerpt from pages 70-71.

When two lineages share what appears to be an arbitrary genetic accident, the case for common descent becomes compelling, just as the case for plagiarism becomes overpowering when one writer makes the same unusual misspellings of another, within a copy of the same words. That sort of evidence is seen in the genomes of chimps and chimpanzees. For example, both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C. As a result, neither humans nor chimps can make their own vitamin C. If an ancestor of the two species originally sustained the mutation and then passed it to both descendant species, that would neatly explain the situation.

More compelling evidence for the shared ancestry of humans and other primates comes from their hemoglobin—not just their working hemoglobin, but a broken hemoglobin gene, too. .... In the region between the two gamma genes and a gene that works after birth, human DNA contains a broken gene (called a "psedugoene") that closely resembles a working gene for a beta chain, but has features in its sequence that preclude it from coding successfully for a protein.

Chimp DNA has a very similar pseudogene at the same position. The beginning of the human pseudogene has two particular changes in two nucleotides that seem to deactivate the gene. The chimp pseudogene has the exact same changes. A bit further down in the human pseudogene is a deletion mutation, where one particular letter is missing. For technical reasons, the deletion irrevocably messes up the gene's coding. The very same letter is missing in the chimp gene. Toward the end of the human pseduogene another letter is missing. The chimp pseudogene is missing it, too.

The same mistakes in the same gene in the same positions of both human and chimp DNA. If a common ancestor first sustained the mutational mistakes and subsequently gave rise to those two modern species, that would very readily account for why both species have them now. It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans.

That strong evidence from the pseudogene points well beyond the ancestry of humans. Despite some remaining puzzles, there's no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives.

Behe and Collins are on the same page. They both recognize the powerful genetic evidence of common descent (macroevolution).

I wonder if Jonathan Wells and Michael Behe talk to each other? I'd love to be a fly on the wall.

Francis Collins and the National Institutes of Health (USA)

After many years of service as director of the National Human Genome Research Institute (NHGRI), Francis Collins resigned from NIH last year. His reasons for quitting were widely reported in the media. Here's the press release from NIH [Francis S. Collins to Step Down as Director of National Human Genome Research Institute].

Dr. Collins explained that his decision to step down as leader of NHGRI came after much personal deliberation. "My decision was driven by a desire for an interval of time dedicated to writing, reflection and exploration of other professional opportunities in the public or private sectors," he said. "The demands and responsibilities of directing an NIH institute do not allow the time commitment necessary for this. In addition, I may need greater latitude than my current position allows to pursue other potential positions of service without encountering any possible conflicts of interest, whether real or perceived."

We now know that the "real or perceived" conflict of interest relates to the creation of The BioLogos Foundation. Here's the mission statement.

Dr. Francis Collins established The BioLogos Foundation to address the escalating culture war between science and faith in the United States. On one end of the spectrum, “new atheists” argue that science removes the need for God. On the other end, religious fundamentalists argue that the Bible requires us to reject much of modern science. Many people - including scientists and believers in God - do not find these extreme options attractive.

BioLogos represents the harmony of science and faith. It addresses the central themes of science and religion and emphasizes the compatibility of Christian faith with scientific discoveries about the origins of the universe and life. To communicate this message to the general public and add to the ongoing dialog, The BioLogos Foundation created BioLogos.org.

Funded by a grant from the John Templeton Foundation, the Web site is a reliable source of scholarly thought on contemporary issues in science and faith that highlights the compatibility of modern science with traditional Christian beliefs. BioLogos.org features responses to a myriad of questions received by Collins, author of The Language of God, Karl Giberson, author of Saving Darwin, and Darrel Falk, author of Coming to Peace With Science since the publication of their books.

It's pretty obvious why running such a foundation is not compatible with a leadership role at the National Institutes of Health (NIH).

That's what makes this report in Scientific American so disturbing [Former Human Genome Project leader Francis Collins likely next NIH director].

The National Institutes of Health (NIH) will likely bring on geneticist Francis Collins, leader of the Human Genome Project, as its new director, Bloomberg News reported on Saturday.

The agency, which has been run by acting director Raynard Kington since October 2008 after Elias Zerhouni stepped down, is in late stages of screening Collins, noted Bloomberg.

Fortunately, we can be confident that the rumor isn't true. With Barack Obama as President of the United States, the appointment of someone like Francis Collins should never happen. Things are going to change in Washington.

Wouldn't it be ironic if the rumor were true and the new head of NIH did not have the enthusiastic support of most scientists? That's the sort of thing that happened under the previous President.

Lies, Damn Lies, etc

Thomas Baekdal advises his clients on how to communicate in the 21st Century. He has posted an analysis of current sources of information and his predictions for the future on his blog baekdal.com: Market of Information: Where Is Everybody?.

Here's the graph that everyone's raving about ...

According to Thomas Baekdal, our society is already getting almost 75% of its information from the internet. By 2020 it will be 90%, according to Baekdal.

The surprising thing about this nonsense is the number of people who believe it.¹ The Web 2.0 cult and its various sects have grown into a kind of social movement populated mainly by people under thirty years old, as far as I can tell. These people are predicting that the world will be radically changed in just a few years as newspapers, books, television, and radio die off. They believe that most citizens will be getting all their information from social networks, social news, blogs and websites.

It's reasonable to ask how such predictions are made and, to their credit, some of the people commenting on baekdal.com have asked. Tom Baekdal replies in comment #30.

The graph was based on combination of a lot of things, a number of interviews, general study, general trend movements, my experience etc. I cannot give you a specific source though, because I used none specifically.

The graphs before 1990 are all based on interviews, and a large number of Google searches to learn about the history of Newspaper, TV and Radio - and more specifically, what people uses in the past. The graphs from 1998 and up to today, is based on all the things that have happened in the past 11 years, of which I have probably seen 1000 surveys ( it is what I do for a living). And the graph from 2009 and forward is based on what I, and many other people predict will happen in the years to come.

One very important thing though, this is not a reflection of my opinion. This is the result a careful analysis. There are always variations, and different types of people. But I believe that this graph accurately reflects consumer focus.

That's it folks. This "careful analysis" is what he does for a living and it is NOT just a reflection of his personal opinion.

It sounds to me a lot like the Oprah Winfrey sort of reasoning that we all respect so highly (not!). This is a dangerous trend. What we're seeing here is the abandonment of rational thought in favor of personal experience, wishful thinking, and pseudo-intellectual, scientific-looking analyses.

Nobody doubts that the internet plays an important role in the lives of many people—this is a blog, after all, and it's really, really important.

Nobody doubts that the internet will take up a larger percentage of people's time in the future. But the change will be incremental and supplemental, just as radio, television, email, and cell phones, became part of our lives without transforming them. Newspapers, magazines, and books did not disappear when every home acquired a radio in the 1930s or a television set in the 1960s and they won't disappear when every home has a personal computer.

I tell by students to look at those big boxes hanging from the ceiling in their classroom. They're from 1969 when everyone predicted that television would take over the classroom. My building was even designed with a television studio on the main floor. It's now offices for research administration.

If it's true that in a few short years we will get 90% of our information from the internet then we need to be afraid, very afraid.

The business world will adapt to incremental changes in the way we communicate and gather information. But the proper response is to base business decisions on real scientific analysis of current trends and behaviors and not on the wishful thinking of someone who makes a living by promoting the death of traditional media.

One of the advantages of being an old foggy is that I've lived through several cycles of so-called "futurists" who are convinced they are the prophets of change (e.g. Alvin Toffler, author of Future Shock, 1970; and George Gilder, co-founder of the Discovery Institute). It gets a bit boring after the first fifty years.

1. That means you, Bertalan Meskó of ScienceRoll

Tuesday, May 26, 2009

Happy Towel Day!

Yesterday was Towel Day in honor of Douglas Adams.

The photograph is from the streets of Innsbruck, Austria, in 2005. That's where Adams got the idea to write The Hitchhiker's Guide to the Galaxy.

He hoped and prayed that there wasn't an afterlife. Then he realized there was a contradiction involved here and merely hoped that there wasn't an afterlife.
Douglas Adams

Monday's Molecule #123: Winners

UPDATE: The "molecule" is a normal electrocardiograph (ECG) of a human heartbeat [see Wikipedia: Electrocardiography]. The Nobel Laureate is Willem Einthoven.

There were eight responses in the first hour. The winner is Òscar Reig of Barcelona! This is our first European winner in many months. I guess I'll have to start posting Monday's Molecule much earlier in the day to give Europe a chance. (Australia doesn't get a chance.)

The undergraduate winner is Maria Altshuler of the University of Toronto who just became eligible after winning last month. Congratulations to Òscar and Maria.

This week there were four Europeans and one South American in the hunt. Not only do my Canadian friends need to be worried, but the Americans are also being challenged! I even had a correct entry from Singapore. That presents a real challenge when I try to calculate the winning time. Why can't they use the same day we use?

You've probably noticed already that today's "molecule" isn't exactly a molecule. That's OK, you can still try to guess what it is. I want a fairly complete description of what you see here. This is supposed to be easy in order to encourage some new readers to enter the contest. There was no winner last week!!!

There's a Nobel Prize associated with this diagram.

The first person to describe the graph and identify the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are five ineligible candidates for this week's reward: Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., and Michael Clarkson of Waltham MA (USA).

The Americans have pulled ahead of the Canadians and the rest of the world is being shut out. Where are the Europeans? Are they just stupid or don't any of them stay up late? BTW, I want to thank all those smart Canadians who have been holding back in order to give the rest of the world a chance.

I still have one extra free lunch donated by a previous winner (Michael Clarkson) to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

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 Prizes 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.

Comments will be blocked for 24 hours.

Denyse Hears Lawrence Krauss

Denyse O'Leary is in Sudbury attending the Canadian Science Writers Conference. One of the speakers was Lawrence Krauss&mdahs;who is speaking in Toronto tomorrow evening.

Here's how Denyse reports on what she heard [Science writing: There are not - repeat, NOT - two sides to the story].

Dr. Krauss went on to say that there is an innate tension between journalism and science. The problem is, “journalists think there are two sides to every story.” According to him, this is not true: “Most times, one side is simply wrong.”

Oh well, that’s all right then. Having been informed that one side is simply wrong, the journalist can forget about getting a range of opinion and simply act as a shill for the approved view.

The beauty of that strategy is that if there are problems with the approved view, the journalist is guaranteed never to find out, so she will always be sure she and her sources are right.

Dr. Krauss later conceded that “The editors are the bad guys.” Yes, indeed, in the sense that editors often come up with additional people for us writers to interview, people who offer additional perspectives. They, like us, see most stories as having many sides, not just one, so they are guilty of multiple sins, and we are complicit (when we are doing our job, that is).

The problem with Denyse O'Leary is that she hears but doesn't listen. Krauss said that "most times, one side is simply wrong." He also said that journalists and editors don't get this, they almost always pretend that there are two sides to every story.

Denyse then proves his point.

Brian Switek on the Darwinius Affair

Brian Switek is an undergraduate at Rutgers University in New Jersey (USA). He's the man behind Laelaps.

Brian knows a lot about fossils and the history of life so it's no surprise that he has an opinion about "Ida" the new fossil primate being hyped in the media. Read his article in The Times of London (UK): The dangerous link between science and hype. Brian covers all the bases from whether the science is correct to whether the media hype is justified.

Brian calls himself a science writer and that's a good choice. This is science writing at its very best.

[Photo Credit: Laelaps]

The Perfect Gift

We've all had this problem. Try to choose the perfect gift for your partner without asking their opinion. Chances are, you got yourself in hot water—especially if you're a man choosing for a woman. I still remember¹ buying that cool flash attachment for her 21st birthday ....

It should come as no great surprise that sociologists have studied this phenomenon. Dave Munger at Cognitive Daily has all the details: Why my mom didn't buy me a slot car track for Christmas in 1978, even though I told her that's what I wanted.

The good news is that we aren't alone. The even better news is that women aren't any better at choosing the perfect gift for a man. (It's just that they're less likely to hear about it!)

We've solved the problem in our family. Now we just ask the gift recipient what they want. Last week I got a new GPS system for my car—it was exactly what I wanted for my birthday. How did she know?

1. Because I'm not allowed to forget it!

[Image Credit: How to Choose the Perfect Personalized Sister Gift]

Monday, May 25, 2009

The Fallacy of the Continuum

I once wrote an essay called "Theistic Evolution: The Fallacy of the Middle Ground." The point I was trying to make is that Theistic Evolution does not occupy the middle ground between superstition and rationalism or between science and religion. Theistic evolution is religious, it advocates superstition over rationalism—albeit a milder form of superstition than that of Young Earth Creationists.

Joshua Rosenau supports the evolution/creationism continuum shown in the above diagram [see Creation/evolution continuum, or NCSE is too nice to theists … and to atheists!]. It's from the NCSE website [The Creation/Evolution Continuum].

Josh claims that the continuum is the proper way to illustrate the differences between those who accept evolution and those who don't.

The nice thing about the continuum graphic is that, regardless of its faults, it emphasizes an easily obscured point: one need not set evolution against belief in a deity who acts in the world, and it is possible to move toward acceptance of evolution without moving out of the realm of theistic belief. The continuum oversimplifies by making it seem like there's just one path one might take in doing so, but NCSE is not in the business of endorsing particular religious philosophies, and making an exhaustive list is beyond the scope of the continuum.

He's got one thing right. It is, indeed, possible to move toward rationalism and science without moving out of the realm of theism. What Josh doesn't understand is that there's a breakpoint not shown on the continuum. I've put it on the modified version I show here.

When you view it like this, it's a different sort of diagram. There is a sort of continuum as theists move farther and farther away from the most outrageous forms of anti-science belief. But there's no continuum between science and most forms of religious belief. That's a sharp line.

Is there a reason for spinning the debate in the form of a continuum? Yes, there is ... you've heard it before.

More significantly, the continuum is helpful as a way to reach out to folks who have simply never thought about the issue before, and naively assume there are two camps: one for creationism and the other for evolution. So when forced to choose (as, for instance, by a pollster) they glom onto whichever camp they think best fits them. If the question is asked in a way that frames the decision in terms of science, they'll tend to favor evolution, if framed around religion or morality, they tend to choose creationism (at least in the US). Pointing out that there is a broad and diverse middle ground, that the choice is not nearly so stark, can help people get comfortable accepting evolution before confronting religious issues.

I understand why framing the debate in this way can be helpful to your cause. What I object to is the implication that moving from theism to atheism via agnosticism is a smooth transition. That's just not true and NCSE is very much endorsing a certain philosophical position when it promotes this diagram.

The continuum is a tool, and a useful one. It helps introduce the complexities of the interplay between science and religion to audiences who may simply think that everyone has to choose one or the other. It often surprises audiences to learn that many people do not see a need to choose, do not find an inherent conflict. (Standard disclaimer/troll repellent: Those people might be wrong, and I take no position on that topic.)

No, Josh, that's not true. You are taking a position on that topic. You are saying that one does not have to choose one or the other. You are saying that the view of evolution espoused by Francis Collins differs only in subtle degrees from that espoused by atheist scientists. You must know that isn't true.

As such, the simple tactic of drawing a bridge between what people think of as two mutually exclusive beliefs is pedagogically powerful.

There is no "bridge" between the belief in supernatural being and non-belief in such beings. How can something be "pedagogically powerful" if it's wrong?

An Ethical Question

Eva Amsen was reading a book in a student study lounge when she was asked to participate in a survey [Spent - Review]. The question was ....

It was a short questionnaire about what you would do if you were standing in line at the post office for more than 30 minutes, waiting to mail a package, and someone offered to take you to the front of the line in exchange for $3. Would you pay the three dollars or keep waiting?

My answer is different than Eva's so this got me thinking.

See the poll in the left sidebar. What would you answer?

Is there a "right" answer?

Monday's Molecule #123

The Darwinius Affair Continues to Embarrass

Today's the day we get to see the global event of the century, or is it millennium?. Sometime this evening there will be a TV show on one of the cable channels. It will reveal the astonishing fossil find that proves once and for all that humans have evolved. (Or something like that.)

The Darwinius Affair continues to embarrass everyone, including the creationists.

A friend alerted me to an article in The Bapstist Press (don't ask): Experts: Fossil find exciting but lacks significance . The article quotes certain "experts" including Kurt Wise the creationist who was a graduate student of Stephen Jay Gould.

"It is always exciting to find a well-preserved fossil, especially of something as rarely preserved as a juvenile primate," Wise wrote in a statement to Baptist Press. "The Messel site has generated a large number of spectacular fossils. Although the sediments seem to have been from a lake, it is an unusual one, somehow allowing remarkable preservation of animals both of the lake and the land.

"The unusual conditions of the Messel lake were probably created by a combination of global warmth (a much warmer earth than that of the present day) and the presence of active supervolcanoes (much larger than any known today) -- both a consequence (I believe) of the earth recovering from the effects of Noah's Flood," Wise, professor of science and theology and director of the Center for Science and Theology at Southern Baptist Theological Seminary, said.

There's more than enough embarrassment to go around, however, evolutionists should take heed when Answers in Genesis (AiG) says ....

The group also said the pitch of Ida as the missing link is "full-out sensationalism by people who are bypassing the scientific community with a direct-to-the-public appeal on behalf of Darwinism."

"All of this seems a departure from the normal turn of events, where researchers study their subject and publish their findings, and let the media chips fall where they may," AiG said.

I agree with Answers in Genesis.¹ We handed this to them on a golden platter and they are right to make it into a big deal. Shame, shame on all the scientists and media types who turned this minor, but interesting, discovery into a public-relations disaster.

1. Whew! I never thought I'd say that.

Franzen, J.L., Gingerich, P.D., Habersetzer, J., Hurum, J.H., von Koenigswald, W., et al. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. [doi:10.1371/journal.pone.0005723]

Saturday, May 23, 2009

I'm really, really hoping this is a joke.

Friday, May 22, 2009

No Democrats Allowed at Liberty University

Liberty University has shut down the students Democrats club. You can read all about it on Pharyngula [“Liberty” University really ought to look at the first word in their name].

The email message has been published by the Washington Post. It needs to be widely circulated to illustrate just how Liberty University is treating its students.

From: Hine, Mark (VP Student Affairs)
Sent: Friday, May 15, 2009 1:37 PM
Subject: LU College Democrats

I must inform you that the College democrats' club is no longer going to be recognized as a Liberty University club. We are unable to lend support to a club whose parent organization stands against the moral principles held by Liberty University. I expressed these concerns when we met, earlier in the spring semester.

The Liberty Way states, "It is the duty of every student to respect Liberty's Statement of Doctrine and Purpose. They may not engage in any activity on or off campus that would compromise the testimony or reputation of the University or cause disruption to Liberty's Christian learning environment."

The Liberty University School of Law had been working on a policy to govern their clubs and organizations for quite some time. They have now completed that policy and we have adopted it for Liberty University as well. Now that it has been adopted and will apply to all clubs and organizations, it is clear that this club does not comply.

Below is a copy of the policy which governs clubs and organizations at Liberty University. This policy is posted on the website.
STUDENT CLUBS AND ORGANIZATIONS POLICIES

Student clubs or organizations must request and receive permission from the Liberty University administration before they may meet on campus, advertise, distribute or post materials, or use any University facilities for their activities or events. All such clubs or organizations and their activities or events must be consistent with the University's mission, and must be and remain in compliance with the Liberty Way, the Honor Code, and any policies or procedures promulgated by the University. The University reserves the right to refuse the use of its facilities for any reason to any student club, organization, activity or event.

Consistent with the Honor Code, all students, student clubs and organizations, faculty and staff of Liberty University, have a responsibility to uphold the moral and ethical standards of this institution and personally confront those who do not.

No student club or organization shall be approved, recognized or permitted to meet on campus, advertise, distribute or post materials, or use University facilities if the statements, positions, doctrines, policies, constitutions, bylaws, platforms, activities or events of such club or organization, its parent, affiliate, chapter or similarly named group (even if the similarly named group is not the actual parent, affiliate or chapter) are inconsistent or in conflict with the distinctly Christian mission of the University, the Liberty Way, the Honor Code, or the policies and procedures promulgated by the University.
Even though this club may not support the more radical planks of the democratic party, the democratic party is still the parent organization of the club on campus. The Democratic Party Platform is contrary to the mission of LU and to Christian doctrine (supports abortion, federal funding of abortion, advocates repeal of the federal Defense of Marriage Act, promotes the "LGBT" agenda, Hate Crimes, which include sexual orientation and gender identity, socialism, etc). The candidates this club supports uphold the Platform and implement it. The candidates supported are directly contrary to the mission of LU. By using LU or Liberty University and Democrat in the name, the two are associated and the goals of both run in opposite directions.

We are removing the club from the Liberty website and you will need to cease using Liberty University's name, including any logo, seal or mark of Liberty University. They are not to be used in any of your publications, electronic or internet, including but not limited to, any website, Facebook, Twitter or any other such publication.

If you have questions please do not hesitate to contact me.

Mark Hine
VP for Student Affairs
Liberty University

This is just the beginning. Mark my words. In a few weeks they're going to shut down the "Liberty University Gays and Lesbians Club" and the "Liberty University Secular Humanist Club." And it's only a matter of time before the "Liberty University Teletubbies Fan Club" is kicked off campus.

Teaching Evolution in Natural History Museums

In an article published last November in Trends in Ecology & Evolution, Bruce MacFadden urges that natural history museums explore the use of new displays, such as those involving genomics and molecular biology, to educate the general public [Evolution, museums and society].

He writes ...

Public understanding of evolution has changed little over the past quarter-century [4]. The challenge therefore remains for natural history museums to improve communication about evolution, particularly the more difficult concepts.

MacFadden notes that museum visitors are more likely to accept evolution. Museums need to do a better job of taking advantage of this fact in order to enhance understanding of evolution.

Evolution represents a complex array of concepts, some of which are well understood whereas others are poorly understood by museum visitors. If an institution is committed to improving public understanding about evolution, then additional resources and effort should be directed toward more effectively communicating the more poorly understood concepts such as natural selection.

Yes, natural selection is difficult but random genetic drift is even more difficult. Unfortunately, I don't get the impression that MacFadden is counting random genetic drift as one of the basic concepts that museum visitors need to learn about.

One solution is to create displays about molecular evolution.

In this regard, there is much room to highlight research traditionally not considered to be natural history, such as genomics and molecular biology [9], although these subjects are not usually specimen based and therefore potentially less attractive to the public. In these instances, visitors are more likely to grasp difficult concepts when they have some prior understanding of a topic [10], or can place these concepts in a modern-day societal context. For example, disease vectors such as influenza and malaria mutate rapidly to become drug resistant, and therefore have negative consequences for world health.

This is a good idea. I recently visited the American Natural History Museum in New York and it had an excellent display on molecular evolution. It showed how you could compare DNA sequences and it explained that many of the mutations were just accidents that became fixed in the population by genetic drift. It even mentioned junk DNA and messy genomes.

It was a very popular display. Not only did it highlight some of the most important evidence for the history of life, it also explained the two main mechanisms of evolution. There were more people reading the material in the molecular evolution area than in the more traditional fossil areas. DNA is exciting.

Kotiaho et al. (2009) disagree. In the June issue of Trends in Ecology & Evolution they write [Evolution education in natural history museums ] ...

In his essay, MacFadden advocates the allocation of resources into novel contents, such as genomics or molecular biology, in order to increase the public understanding of evolution. We argue that museums should concentrate more on demonstrating the basic principles and outcomes of natural selection, rather than presenting fashionable novel contents such as genomics (which, it seems, even scientists often have a hard time understanding [4]).

It's clear that Kotaiho et al. see natural selection as the main (only?) mechanism of evolution. What they want is the kind of display that illustrates natural selection. They like dioramas.

If we want to educate the visitors of natural history museums about evolution by means of natural selection, we should aim at delivering the message that across species there is enormous within-species variation, that some of this variation is likely to cause differences among individuals in their lifetime reproductive success and that these differences will result in a constant change – evolution. In museums, we have a great opportunity to do this; as well as the exhibits open to the public, museums usually have extensive collections containing numerous individuals of each species. A simple illustration of the replacement of one generation by the next generation might work in making the operation of natural selection more tangible. With such an illustration, we can easily see why and how a population can undergo constant change, and thus grasp the basic principles of evolution by means of natural selection.

Natural history museums are our collective memory of the past. Their collections can, and have been, used to study evolution (e.g. [7]). Perhaps even more importantly, however, they could also be used to illustrate to the general public the evolutionary changes that have taken place. We challenge the exhibit designers of natural history museums to emphasize variation within species, and to demonstrate change due to natural selection, rather than stasis in nature.

Here's the problem. It might be fine to mount a display showing variation within a population. It might be possible to construct a display where the next generation has a different degree of variation. But it would be wrong to attribute that to natural selection unless you could present evidence that there were fitness differences associated with those variants.

I fear that these authors are not distinguishing between evolution and natural selection. They think that evidence of evolution is evidence of natural selection.

I don't understand why Kotaiho et al. would want to ignore molecular evolution and genomics. There's no better way to illustrate random genetic drift and there's no excuse for eliminating one of the most important fields in modern evolutionary biology.

Thursday, May 21, 2009

The Darwinius Affair

The Darwinius Affair is getting messier. Not only did some scientists commit a serious breach of scientific ethics by exaggerating their claims about the fossil, but they also prevented legitimate science journalists from doing their job.

As most of you know, I think that science journalists should examine the claims of scientists in order to ensure they are accurate. They should not just take the word of the scientist, no matter how famous he or she is.¹

In order to do their job, the science journalists need access to the scientific paper before it is released to the public. This is standard practice. Journalists are used to, and respect, news embargos.

In this particular case, it appears that scientists and the editors of PLoS ONE prevented journalists from seeing the paper until the press conference and all the associated hoopla was under way. Carl Zimmer has the story at Science Held Hostage.

Shame on PloS ONE, on the scientists who wrote the paper, and on everyone else who is associated with this media event. This is not how science is supposed to work. This is not how we should be communicating with the general public.

Franzen, J.L., Gingerich, P.D., Habersetzer, J., Hurum, J.H., von Koenigswald, W., et al. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. [doi:10.1371/journal.pone.0005723]

1. Most professional science journalists don't do this, but that's another issue.

Wednesday, May 20, 2009

It's that time of year, again.

The course is over, the exam has been written, the marking is done, and the grades have been submitted. There's a short lag while the marks are checked and then they're posted so that students can learn how they've done in the course.

At my university we submit grades as percentages. They are converted to grade points (out of 4) in order to calculate a grade point average. The percent score is reported on the transcript and so is the grade point average. ~~A mark of 76% is a 3.0, a mark of 77% is a 3.5 and a mark of 80% is a 3.7.~~ A mark of 76% is a 3.0, a mark of 77%-84% is a 3.7, and a mark of 85% or above is a 4.0. There is no 3.5—shows you how much attention I pay to those sorts of things.

The email messages start as soon as the marks are posted. Every year there are students who want more marks. Usually it's just a few more marks to raise their grade points from 3.3 to 3.7 or something similar. That's by far the most common request. Sometimes the student wants lots more marks because they worked really hard in the course and deserve a much higher grade.

The most common reasons for asking for more marks are ...

losing a scholarship
not going to get into medical school/graduate school
grade doesn't reflect effort
parents will be disappointed
the final exam was unfair
student wasn't feeling well during the test that gave the lowest score
this is the lowest grade ever received

Some of the letters just ask me to give them more marks because I feel sorry for them. But many contain the suggestion that they are willing to pay for a higher grade. Fortunately, I can handle all these requests by just referring students to the standard appeal process. Once the grades are submitted to the Faculty I can't change them. It's one of the few times that I like the rules and regulations.

Every Professor in the Department gets these requests at this time of the year.

Here's the important part—it's not fair to put the entire blame on the students. There's something about the way we run the university that makes it seem acceptable to beg for higher marks. What are we doing wrong? How can we fix it?

I have a trivial solution that will deal with many of the problems.

ABOLISH GRADE POINTS AND GRADE POINT AVERAGES

Nobel Laureate: Charles Robert Richet

The Nobel Prize in Physiology or Medicine 1913

"in recognition of his work on anaphylaxis"

Charles Robert Richet (1850 - 1935) won the Noble Prize in 1913 for discovering the phenomenon known as anaphylaxis. This is a condition where the administration of an antigen causes severe symptoms, even death. Richet found that anaphylactic shock occurs only after an animal had been previously immunized and even then only after some days had passed.

It appeared as though the first immunization took several days to develop but when the process was complete a second attempt at boosting immunization causes a severe reaction. Anaphylactic shock was rare, it only happens in a small percentage of cases. We are familiar with the risk when people are known to be allergic to peanuts or insect stings.

Today we know what causes the symptoms of anaphylaxis; it's due to massive release of histamines, prostaglandins, and leukotrienes from mast cells. The release of these chemicals produces rapid heartbeat, sweating, and constriction of the airways. The symptoms can be relieved, and death prevented, by rapid treatment with epinephrine.

The primary cause of most anaphyaxis is overproduction of antigen-specific immunoglobulin E (IgE) molecules on the mast cells.¹ It's the IgE molecules that interact with the antigen to cause release of histamines etc. It's not known why some antigens lead to overproduction of IgE such that subsequent exposure to the same antigen cause a massive allergic reaction. (Normal antibodies are immunoglobulin G or IgG.²)

Immunology is complicated. That's why we can't cure asthma and other allergic reactions even though the phenomena have been intensely studied for more than 100 years.

Here's an excerpt from the 1913 Presentation Speech.
THEME:
Nobel Laureates

In an age in which the leading members of the medical profession tend to concentrate on innumerable experiments demonstrating the growing immunity of the organism towards poisons already resisted successfully once, you, Sir, have found that in certain cases a completely opposite result is produced. You did not restrict yourself to this isolated observation: studied in depth by you, it has become the foundation on which you have based the evidence of a reaction that is sometimes just as regular as the phenomenon of immunity. We are not concerned solely with specific prophylaxis; thanks to you, we are now aware of a specific anaphylaxis.

We do not discount the work of those who, following your lead, have observed similar phenomena, but to you goes the honour of having established the basis of a new biological reaction, anaphylaxis, and of having been the first to demonstrate it clearly. Thereby you have opened up to medical science an enormous field of study as yet unexplored. The Staff of Professors of the Caroline Institute wishes to reward you for this achievement by conferring on you the prize instituted by our compatriot Alfred Nobel for those «who have made the most important discovery in the field of physiology or medicine».

Please accept the warm congratulations of the Institute and myself, together with the wish of us all that success will continue to crown your devoted work.

1. I do not mean to imply that IgE molecules are produced by mast cells. They are not.

2. There are several different classes (isotypes) of antibodies; IgG, IgD, IgM, IgA, and IgE. The most abundance class is IgG—that's the one most often depicted in the textbooks. It's probably the type most people think about when they think about antibodies. I did not mean to imply that the other classes are not "normal."

[Photo Credit: Wikipedia]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Science Journalism at its Worst

This video is an embarrassment. At a time when we are trying to convince the public that science is credible, along comes a trashy exploitation that sets science back several decades.

This is not how science works. It is not accurate science and it is not an accurate depiction of how scientists will react to the discovery of Darwinius masillae.

Cafe Inquiry: Freedom of Speech and the Atheist Bus Campaign

Join us on Friday night for a discussion about Freedom of Speech and the Atheist Bus Campaign.

Modeled on the highly popular Cafe Scientifique, Centre for Inquiry presents Cafe Inquiry. Join us for a series of interactive forums exploring contemporary issues in science, reason, philosophy and politics. We bring you 2 or 3 guest experts that open by addressing the issue from a variety of perspectives and responding to moderator questions. Then we open it to the floor for your questions and comments to the panel and each other. This is your chance to interact with a diverse group of people on CFI's broad topics.

I've met some of the people who were involved in the atheist bus campaign. This promises to be a fun evening. If you've never been to an event at the Centre for Inquiry you can get in touch with me. I'll be happy to meet up with you and take you to the location.

What Fools Those Atheists Be!

Read Lord! What Fools Those Atheists Be! in Report Magazine. (Report Magazine is published in Edmonton, ~~Texas~~ Alberta. It bills itself as "Western Canada's Conservative Voice.") The author of the offensive article is Pastor Shafer Parker, a Texas native who is now with the Hawkwood Baptist Church in Calgary.

Before you read the article, answer the poll question in the left-hand sidebar: "Do you believe that there is a 'God'"? So far, the answer "Absolutely!" is leading over "Absolutely Not!" but it's early days.

Heathen Mike of Mike's Weekly Skeptic Rant has dissected most of the article at: Shafer Parker, Answered. You should read what Mike has to say. I'm sure you'll be convinced that it's not the atheists who are the fools.

Most of Pastor Parker's rant is against the bus ads promoting atheism. I want to address one particular point in Parker's article. He says ...

The Christian West's centuries-old tradition of free expression and open debate is unique in that nothing like it exists anywhere else on earth. No such tradition exists in any society dominated by a single non-Christian faith, including the atheistical Communist-materialist nations of China, North Korea and the former Soviet Union. It is not an accident that these ads have deliberately set out to offend the majority Christian theists living in London, Madrid and Washington, D.C. They would not have been allowed in Beijing, New Delhi or Riyadh.

Parker believes that Christianity is associated with free expression and open debate. He claims that no other religion has a similar tradition. This would have been news to the people of Cordova in the Moorish Kingdom from 800-1200 AD. It would also have been news to most Catholics throughout history and to most Protestant sects (e.g. Puritans). They aren't exactly noted for tolerating free expression and open debate. (Were the ancient Greeks Christians?)

But let's put history aside. It's obviously not one of Parker's strong points. Let's just look at Christian nations in the last century or so. Mussolini's Italy and Franco's Spain come to mind. So does Czarist Russia. I'm sure there are plenty of other Christian nations where free expression and open debate were not common—I'm thinking of several nations in Central and South America. I don't think he's making a valid point. I don't think the concept of free expression is in any way a product of Christianity.

What about modern states? Israel, Japan. and India seem to be non-Christian states that have a certain degree of free expression and open debate. Parker says that the atheist signs would not be allowed on buses in New Delhi. I suspect he's wrong about that. In any case, he ignores the fact that the atheist signs will never be allowed in some of the most Christian parts of America. Isn't that strange?