More Recent Comments

Friday, December 15, 2006

Photos of Gol 737 Mid-Air Accident

 
Friday's Urban Legend from About: Urban Legends and Folklore.


This photograph is supposed to have been taken from inside a plane that has just been involved in a mid-air collision. The plane crashes and everyone on board is killed. The photo was recovered from a digital camera at the crash site.



Status: FALSE
This is a hoax. The photos are from the opening scene of Lost.

We're in Trouble Now

 
According to New Scientist the Biologic Institute in Redmond, Washington is doing research to support Intelligent Design Creationism. The lab's senior reseacher is Douglas Axe and there are at least two other "scientists" on staff.

The active areas of investigation include bacterial metabolism and protein folding. It won't be long now, folks. Look for lots of scientific articles about Intelligent Design Creationism in the scientific journals and for acceptance of intelligent design as legitimate science.

Meanwhile, Santa Claus is coming in less than two weeks.

Thursday, December 14, 2006

Fathers of Stem Cell Research

 
The Toronto Star reports that James Till and Ernest McCulloch were named to the Order of Ontario.

Till and McCulloch, Professors in the Department of Medical Biophysics at the University of Toronto, discovered stem cells in the early 1960's. They are members of the Royal Academy of Sciences, members of the Canadian Medical Hall of Fame, and winners of the Lasker Prize and the Gairdner Award.

When will they get their well-deserved Nobel Prize?

Atheists' bleak alternative

 
Jeff Jacoby of the Boston Globe writes on Atheists' bleak alternative

First, the good news ...
FROM THE land that produced "A Christmas Carol" and Handel's "Messiah," more evidence that Christianity is fading in Western Europe: Nearly 99 percent of Christmas cards sold in Great Britain contain no religious message or imagery.


Now the bad news ....
What is at stake in all this isn't just angels on Christmas cards. What society loses when it discards Judeo-Christian faith and belief in God is something far more difficult to replace: the value system most likely to promote ethical behavior and sustain a decent society. That isbecause without God, the difference between good and evil becomes purely subjective. What makes murder inherently wrong is not that it feels wrong,but that a transcendent Creator to whom we are answerable commands: "Thou shalt not murder." What makes kindness to others inherently right is not that human reason says so, but that God does: "Love thy neighbor as thyself; I am the Lord."

The atheist alternative is a world in which right and wrong are ultimately matters of opinion, and in which we are finally accountable to no one but ourselves. That is anything but a tiding of comfort and joy.
Good Heavens! Another deluded Judeo-Christian. And in Boston no less. How do these idiots manage to survive in a town with more than one traffic light?

Don't go to London, Jeff. The crime rates there must be outta sight.

Lessons from the Culture Wars

 
The little dust-up in Dover Pennsylvania has been over for a year. The judge has ruled that Intelligent Design Creationism (IDC) is just religion dressed up as science. It took a bevy of lawyers and millions of dollars to prove the obvious, but at least the good guys won. Because Intelligent Design Creationism is religious, it cannot be taught in public schools since this would violate the Constitution of the United States of America. That's what the trial was all about.

The Judge Jones Opinion was lengthy (139 pages) and well-written. Like many of you, I was impressed with the way he dissected the arguments from the IDiots. I admired the scholarly approach to complex issues like methodological naturalism (p. 30, 65), philosophical background of intelligent design (p.24, 30), whether IDC was religious (p.28, 30), irreducible complexity (p.74), and the definition of science (p. 64). I was amazed and humbled. Whenever I try to explain some of these things I am attacked by fellow evolutionists for my ignorance of matters philosophical. Judge Jones was widely praised for his brilliance and I thought the praise was amply justified.

Judge Jones listened to hours and hours of testimony. Many of us read the transcripts and listened to summaries of the trial as it progressed. (It lasted six weeks.) It can't have been easy to distill the essence of what the expert witnesses were saying and present it in such a concise and correct manner. I couldn't have done as fine a job, even though I'm quite familiar with the arguments. It seemed to be clear evidence that Judge Jones understood the issues very well. Or so I thought.


Recently I learned that the relevant parts of the Judge Jones document were copied almost word-for-word from another document written by the evolutionist team. This team, which includes many lawyers and consultants, is the plaintiff side of the case. The document is Plaintiffs' Findings of Fact and Conclusions of Law.

(It doesn't really matter to me how I learned of this but, for the record, it was through Casey Luskin, the chief IDiot on the Discovery Institute website. My opinion wouldn't be any different if I had first been told by Nick Matzke, Timothy Sandefur, or Ed Brayton. I mention this because in the ensuing controversy the source of the information, whether accurate or not, seems to make a difference to some people.)

Allow me to quote just one example from the Judge Jones opinion in order to illustrate a point. The argument of intelligent design is superficially attractive to many people and Behe can often explain it very well. Judge Jones listened to the testimony and here's how he summarized this complex topic,
Professor Behe summarized the argument as follows: We infer design when we see parts that are arranged for a purpose. The strength of the inference is quantitative; the more parts that are arranged, the more intricately they interact, the stronger is our confidence in design. The appearance of design in aspects of biology is overwhelming. The appearance of design in aspects of biology is overwhelming. Since nothing other than an intelligent cause has been demonstrated to be able to yield such a strong appearance of design, Darwinian claims notwithstanding, the conclusion that the design seen in life is real design is rationally justified. (18:90-91, 18:109-10 (Behe); 37:50 (Minnich)). As previously indicated, this argument is merely a restatement of the Reverend William Paley’s argument applied at the cell level. Minnich, Behe, and Paley reach the same conclusion, that complex organisms must have been designed using the same reasoning, except that Professors Behe and Minnich refuse to identify the designer, whereas Paley inferred from the presence of design that it was God. (1:6-7 (Miller); 38:44, 57 (Minnich)). Expert testimony revealed that this inductive argument is not scientific and as admitted by Professor Behe, can never be ruled out. (2:40 (Miller); 22:101 (Behe); 3:99 (Miller)).

Indeed, the assertion that design of biological systems can be inferred from the “purposeful arrangement of parts” is based upon an analogy to human design. Because we are able to recognize design of artifacts and objects, according to Professor Behe, that same reasoning can be employed to determine biological design. (18:116-17,23:50 (Behe)). Professor Behe testified that the strength of the analogy depends upon the degree of similarity entailed in the two propositions; however, if this is the test, ID completely fails.
This sounds very impressive. It seems as though Judge Jones was paying attention. He seems to have grasped the essential flaw in Intelligent Design Creationism and honed in on the connection to Paley. This is one of the reasons why I admired the opinion when it was first published.

However, if we look at the Plaintiffs' Findings of Fact and Conclusions of Law, we see that Judge Jones has borrowed extensively from that document. This does not diminish the strength of the argument against Intelligent Design Creationism, but it shifts the attribution for that argument from Jones to the lawyers for the plaintiffs. This is what I mean when I say that I feel as though I've been deceived. I'm one of those people for whom correct attribution is important. I like to credit people who originate ideas rather than people who copy them. Here's the same passage written by the Plaintiffs ...
# 83. Professor Behe summarized the argument as follows: We infer design when we see parts that appear to be arranged for a purpose. The strength of the inference is quantitative; the more parts that are arranged, and the more intricately they interact, the stronger is our confidence in design. The appearance of design in aspects of biology is overwhelming. Since nothing other than an intelligent cause has been demonstrated to be able to yield such a strong appearance of design, Darwinian claims notwithstanding, the conclusion that the design seen in life is real design is rationally justified. 18:90-91 (Behe slides, at 7); 18:109-110. See also, 37:50 (Minnich).

# 84. This is not a new argument, but a restatement of the Reverend William Paley's argument applied at the cell level. 1:6-7 (Miller); 38:44, 57 (Minnich). Minnich, Behe and Paley reach the same conclusion that complex organisms must have been designed using the same reasoning, except that Professors Behe and Minnich refuse to identify the designer, whereas Paley inferred from the presence of design that it was God. Id.

# 85. This inductive argument is not scientific. 2:40 (Miller). As Professor Behe admitted, it can never be ruled out. 22:101. See also, 3:99 (Miller).

# 86. The assertion that design of biological systems can be inferred from the "purposeful arrangement of parts" is based on an analogy to human design. According to Professor Behe, because we are able to recognize design of artifacts and objects, that same reasoning can be employed to determine biological design. 18:116-17; 23:50.

# 87. Professor Behe testified that the strength of an analogy depends on the degree of similarity entailed in the two propositions. 20:69. If this is the test, intelligent design completely fails.
There are numerous overlaps between the two documents covering pages 24-35 and 64-89 of Judge Jones' opinion. Much of the opinion is reproduced word-for-word from the Plaintiffs' Findings of Fact and Conclusions of Law.

Knowing what I know now, I no longer feel comfortable with praising Judge Jones for his brilliance and his understanding of science. What Judge Jones was able to do was to distinguish between the lies and distortions of the IDiot team and the expertise of the evolution team. Having recognized the difference between ignorance and knowledge, Judge Jones choose to copy the work of the smart people and incorporate it into his opinion.

To me, this does not indicate a profound understanding of the issues. It would be comparable to one of my students handing in an essay by Stephen Jay Gould instead of one by Ken Ham. Yes, the student was at least smart enough to recognize the difference between Gould and Ham, but does this count as brilliant? Does it prove that the student understands evolution. I don't think so.

In the past two days I've learned a lot about American culture and American legal ethics and practice. Some of my teachers have taken the time to make comments in the two articles I posted [Judge Jones and the Dover Trial, The Judge Jones Decision]. Others have singled me out on their own blogs, patiently and politely explaining why I am such an ass. But, as usual, the greatest teacher of all is Ed Brayton over at Dispatches from the Culture Wars [Moran Joins the Judge Bashing].

Ed and his followers—a dozen or so at last count—are not happy. Apparently, I have violated one of the cardinal sins of the appeasers. I have questioned one of the good guys. They want to make sure everyone understands the depth of my ignorance. Thanks, Ed, I appreciate the lesson from such an expert. Here's what I've learned. Ed says,
What a patently silly criticism. What does Moran expect, that Judge Jones was going to invent his own arguments? That's not what judges do. When it comes to findings of fact, the judge does nothing more than determine which set of facts presented by the two sides is better supported by the evidence. Having decided that, can it really reasonably be argued that the difference between him being "brilliant" and being something less than brilliant is what percentage of the text he bothered to reword? Of course not.
Yes, indeed I did expect the judge to express his own opinion. Yes, I thought the difference between being "brilliant" and being something less than brilliant has something to do with expressing yourself in your own words. Professors can be picky about that sort of thing.

I now know better. I now know that my expectations were unrealistic. The American legal culture places a high value on the ability to copy the right document and not on the ability to be an original thinker. This is a different culture than I one I inhabit. I'm sorry for being so out-of-step. I understand your culture's definition of "brilliant" and I accept it, even if I disagree.

Ed continues to teach,
Remember, we're talking about maybe 20 pages out of a 139-page decision. We're talking about a set of statements of fact, not legal arguments, where both sides presented their statements and the judge's job is to determine which set is best supported by the evidence presented in the case. Had he made the very same statements, but used different words to say the same thing, would that make the opinion more or less valid? Nope. Does it have anything to do with how well he understood the issues? Not a bit.
Your culture thinks that copying the words of others (or paraphrasing) is a good way of demonstrating how well you understand the issues. Mine doesn't. I understand what you mean by culture wars.

I asked "Now, the question is, who really wrote the ACLU "Finding of Fact?" Did they know from the beginning that the Jones decision had incorporated a lot of their material? If so, why did they leave us with the impression that Judge Jones "has taken the time to really understand not just the legal issues, but the scientific ones as well?" Ed answers,
Well Larry, I can answer those questions. The findings of fact were writen by the legal team,working with the various consultants in the case who were helping them on the scientific side (the expert witnesses, the NCSE staff, and even some others in our broader community). Every single one of us knew that the ruling had closely followed the proposed findings of fact.
I take this to mean that you were aware from the beginning that large sections of the Judge Jones opinion were reproduced exactly as found in the plaintiffs' document. Point taken. It seems to be common knowledge among Americans that judge's opinions are not necessarily written by the judge. It seems to have been widely known that Judge Jones copied large sections of the plaintiff's document. Dozens of people have criticized me for not knowing this. Mea culpa. I didn't know, but apparently I should have.
There are only two kinds of people who could claim to find this "study" in any way surprising or distressing: demagogues (like the DI) and those who simply aren't aware that this is the entire purpose of filing proposed findings of fact and is absolutely normal. Why on earth do they think those proposed findings are written in the judge's voice? Because it is normal and expected that whichever argument the judge determines is true, the court's findings of fact are going to be very similar to the winning side's findings of fact.
Put me in the category of not knowing that this process of extensive copying is absolutely normal in American courts. Put me in the category of not knowing enough about how your culture defines "brilliance" and "understanding of science." I hope this clears up any confusion. I was stupid, but I'm not a demagogue.
What all this ignorant blather, by both the DI and by Moran, comes down to is the ridiculous assertion that once the judge determined which statements of fact were correct and best supported by the evidential record in the trial, he should have reworded more of those arguments more often and more severely than he did, and that failure to do so undermines either the validity of his ruling or his intelligence.
Enough, Ed. I never said that the validity of his ruling was in question. I'm in no position to judge the minutiae of American constitutional law. One of the things that I didn't know was that a judge can just copy the arguments of one side and claim them as his own. I also didn't know that in your culture this can be a sign of intelligence, even brilliance. It explains a lot. Thanks for the lesson.
I can understand why the DI takes this position; hell, they have to. What else do they have other than cheap attacks? But I can't for the life of me understand why Moran would join them in their absurd attacks. The DI threw out this rotting carcas of nonsense as bait and Moran swallowed it hook, line and sinker. Worse yet, he's using his ignorant misunderstanding of the legal process as a pretext for attacking the character of those of us who wrote about the trial and claim that we were covering up this absolute non-story.
Chalk it up to ignorance, Ed. I was ignorant of the way you do things down there and of your standards for brilliance. I'll try not to overestimate you again.
As I said before, with friends like these...
Friends are allowed to disagree. It's healthy. I've just learned a lot about your culture and your intellectual standards. Did you learn anything about mine?

Wednesday, December 13, 2006

Biochemistry With the Celebrity Stars

 
Late Night with Conan O'Brien presents Biochemistry With the Stars.

Nobel Laureates: Hermann Emil Fischer

 
The Nobel Prize in Chemistry 1902.

"in recognition of the extraordinary services he has rendered by his work on sugar and purine syntheses"

Emil Fischer (1852-1919) (not to be confused with Hans Fischer) is most famous for "Fischer projections," a way of depicting three dimensional molecules in two dimensions. He won the first Nobel Prize in Chemistry for his work on the structure of sugars and purines.

Purines, are essential components of nucleic acids but Fischer was much more interested in caffeine and theobromine, the active chemicals in coffee and cocoa. He predicted that coffee and chocolate would be replaced by completely artificial bags of chemicals that would be just as satisfying as the real thing.

Here's an image from his Noble Lecture showing the various purines that could be synthesized from guano (bird droppings).

neurophilosopher, me, and PZ

 
The Neurophilosopher reminds me that he doesn't have a picture of him on the Sandwalk (yet) but he has the next best thing. He, me, and PZ in front of the Natural History Museum in London. The photo was taken by a young man who had no idea how famous the photo would become.

Monday's Molecule #5

 
Name this molecule. You must be specific. We need the exact name and why it's important in every living cell. Comments will be blocked for 24 hours. Comments are now open. Answer tomorrow. See below for the answer.

The molecule is N-carboxyaminoimidazole ribonucleotide. Three people, "dunbar," Steve LaBonne, and "Martin S." got the right answer. N-carboxyaminoimidazole ribonucleotide is an essential intermediate in the pathway to purine synthesis in most cells. Purines are needed to make DNA and RNA. See below the fold to find out if you need this molecule ....


The relevant part of the pathway begins with aminoimidazole ribonucleotide (AIR). It is converted to N-carboxyaminoimidazole ribonucleotide in a CO2 (in the form of bicarbonate) fixing reaction that requires ATP. In the second step, the carboxylate group is shifted from the nitrogen atom to the carbon atom in the ring forming carboxyaminoimidazole ribonucleotide (CAIR). The newly added carbon atom will become C-6 of the completed purine ring.

In prokaryote, these two steps are catalyzed by separate enzymes. In eukaryotes, the two enzymes have become fused to form a single large multifunctional enzyme that can carry out both steps. In vertebrates, it is thought that a single enzyme (AIR carboxylase) can transfer bicarbonate directly to create CAIR. This conclusion is based on a single 1994 paper that studied the chicken enzyme. As far as I know it hasn't been confirmed.


A Bar Fight Over ATP!!!

 
A.J. Milne over at The Accidental Weblog got into a fight in a bar on Monday night. The cause? ... whether ATP had higher energy than ADP [Why are you wincing?].

This has got to be a first. Only in Canada.

Tuesday, December 12, 2006

The Judge Jones Decision

 
Nick Matzke was kind enough to send along a link to a radio talk show taped on December 22, 2005—just a few days after the Jones decision was handed down. Thanks Nick.

Casey Luskin, chief IDiot at the Discovery Institute was also on the show. Nick brags that Jones accepted almost every argument the good guys made. I don't actually hear him saying that Jones copied text directly from the ACLU Findings brief but perhaps I missed it. Nevertheless, the information was out there. Casey Luskin certainly knew of it a year ago.

I wish I'd known. It would have changed my opinion of Judge Jones. I now see him as a good judge but not necessarily an intellectual with an amazing ability to write about complex isues in science and philosophy.

Deluded Irish Catholics Challenge Dawkins

 

"Non-Confidence" on Afghanistan

 
The Conservative government of Stephen Harper might fall on the issue of Afghanistan. The leader of the Bloc Quebecois is threatening a non-confidence motion on Afghanistan when parliament resumes after the Christmas break. The other parties are making noises about supporting the motion, in which case the minority government will fall.

The issue concerns the role of Canadian forces in Afghanistan. Is this a war that can be won? Is too much effort being paid to search-and-destroy missions against the insurgents and not enough to rebuilding?

I don't think Canada belongs in a country where the citizens don't want us. A country that's controlled by opium warlords who are little better than the Taliban. A country where thousands of insurgents enjoy safe haven in Pakistan. I hope the motion passes and we get out as soon as possible.

Studio 60 Tribute to New Orleans

 
I love "Studio 60 on the Sunset Strip." I hope it doesn't get cancelled.

The Tribute to New Orleans clip is up on the Studio 60 website. If you haven't seen it, go there right now.

Editorial Terrorism

 
Some of us have been victims of editorial terrorism. This is when you send off your perfect masterpiece to some editor in Indiana and it comes back full of cryptic markings in a foreign language. The only thing you know for sure is that the editor didn't like your manuscript.

Well, it turns out those scratchings actually mean something. They're called Proofreader's Marks. Who woulda thunk?

Judge Jones & the Dover Trial

 
When the Jones decision was first published I read every word. I was very impressed. Here was a man who seemed to have learned a lot of sophisticated science in a very short period of time. His grasp of complexities like the evolution of bacteria flagella and blood clotting was impressive. His understanding of the meaning of science rivaled that of many advisors on the ACLU side. Frankly, I was jealous, and humbled.

Everyone was praising the Jones decision. For example, Timothy Sandefur on Panda's Thumb wrote,
Kitzmiller v. Dover Area School District is a major victory for science and a major blow to those who have tried to sneak religion into the classroom by disguising in scientific garb. But it’s more than that. It is a brilliant, insightful, profound decision that reaches to the bottom of ID and finds it empty.

Judge John Jones, a George W. Bush appointee, deserves the praise and thanks of every defender of rigorous, meaningful scientific education. He has taken the time to really understand not just the legal issues, but the scientific ones as well. This decision proves he is a credit to the federal judiciary.
These comments, and others, seemed to confirm that Jones had written this decision all by himself and deserved full credit for his brilliant analysis.

As it turns out, this isn't true and I feel deceived.


The Discovery Institute is reporting that the "Masterful" Federal Ruling on Intelligent Design Was Copied from ACLU and Timothy Sandefur acknowledges that this is true [Weekend at Behe's].

Apparently Judge Jones copied the most "scientific" parts of his decision from the ACLU ‘Findings of Fact and Conclusions of Law’ that was submitted a month before the decision was published. I'm told that this is standard practice. Judges often rely heavily on written submissions from the side they support. I'm told that it's common for judges to copy from those submissions.

That may be true—I have no reason to doubt it—but it does make a difference to me. The legal significance of the decision doesn't change but my opinion of Judge Jones does. He is no longer the brilliant man who was able to grasp complex scientific concepts in the blink of an eye. He's able to discern who's right and who's wrong, but that's all.

Now, the question is, who really wrote the ACLU "Finding of Fact?" Did they know from the beginning that the Jones decision had incorporated a lot of their material? If so, why did they leave us with the impression that Judge Jones "has taken the time to really understand not just the legal issues, but the scientific ones as well?"

E. coli O157:H7 Outbreak in Taco Bell Restaurants

 
The Centers for Disease Control and Prevention reports that 64 people have been hospitalized as a result of bacterial infection arising from contamination at Taco Bell restaurants in New York, Pennsylvania, New Jersey, and Delaware. Of these patients, 38 have been confirmed as E. coli strain O157:H7 infections. All of these patients have been infected with the same substrain as determined by DNA fingerprinting.

What this means is that all infections arose from a single source. There must be something in common among the restaurants in all four states. A preliminary analysis detected E. coli O157:H7 contamination of green onions in one of the restaurants but DNA fingerprinting showed that it was a different substrain, proving that this was not the soure of infection.

DNA fingerprinting is a powerful tool in tracing outbreaks of toxic bacteria. It also proves evolution. How is it done?

The figure below is an example of DNA fingerprinting from the following paper.
Hahma, B-K., Maldonadob, Y., Schreiberc, E., Bhuniab, A.K. and Nakatsua, C.H. (2003) Subtyping of foodborne and environmental isolates of Escherichia coli by multiplex-PCR, rep-PCR, PFGE, ribotyping and AFLP. Journal of Microbiological Methods 53; 387-399.

There are several different ways of making DNA fingerprints. In the one shown here, DNA is extracted from each substrain of bacteria and digested with a restriction enzyme called Xba I. This enzyme chops the DNA at specific sites in the genome corresponding to the DNA sequence TCTAGA. The result is that the genomic DNA is cut into large pieces of different sizes, ranging from about 100,000 base pairs (bp) to 500,000 base pairs (or 500kb). Since the whole genome of E. coli is about 4,600,000 bp in size, this means the there will be something like 20 DNA fragments produced by cutting with the enzyme.

The DNA fragments from different strains will show differences in sizes whenever the genome has been altered by the insertion of new DNA or the deletion of some existing DNA. These insertion/deletion events occur quite frequently in evolving populations as we saw recently in work done on human populations.

A solution containing the collection of fragments from a single strain is put on the top of an agarose gel and a strong pulsed field electric current is applied. Since DNA is negatively charged, the fragments will move into the gel and separate according to size—smaller fragments will move faster. In the example shown, the top of the gel is on the right and the bottom is on the left.

The large open bracket at the top right of the image covers various O157:H7 strains. The evolutionary tree on the left shows how this strain is related to other E. coli strains at the bottom of the image. Within the O157:H7 strains there are many serotypes that have descended recently from a common ancestor. Each serotype has a unique combination of restriction fragments of different lengths. That's the DNA fingerprint.

Note the cluster that's fourth from the top. It's labelled "Odwalla Juice" after an outbreak that occurred several years ago. (You may not be able to read it in the figure.) There are five lanes with identical DNA fingerprints indicating that these five different isolates (from five different patients) all came from the same source. The same technique is being used to trace the current outbreak.

The Centers for Disease Control and Prevention have already eliminated a number of cases by DNA fingerprinting. These patients are not part of the current outbreak. It's important to concentrate only on those patients that are part of the cluster having a common source and not be confused by other infections. That way, the source can be identified and eliminated.

Not to belabor a point, but none of this would be possible if it weren't for evolution and our understanding of how evolution works.


Monday, December 11, 2006

Stanley Cup Playoffs Are Bad for You!

 
Medical News Today warns us that Stanley Cup Playoffs Can Harm Your Hearing. Well, duh! Smart Toronto residents have known this for decades. That's why we've skipped the Stanley Cup playoffs so often and why we have carefully avoided winning the cup every single year since 1967. According to the latest results (seven losses in a row), the Toronto Maple Leafs are on track to protect us from hearing loss once again.

Kofi Annan's Final Speech

 
Delivered today at the Truman Presidential Library in Independence Missouri. [Full Text from BBC News]
That is why this country has historically been in the vanguard of the global human rights movement. But that lead can only be maintained if America remains true to its principles, including in the struggle against terrorism.

When it appears to abandon its own ideals and objectives, its friends abroad are naturally troubled and confused.

And states need to play by the rules towards each other, as well as towards their own citizens. That can sometimes be inconvenient, but ultimately what matters is not convenience. It is doing the right thing.

No state can make its own actions legitimate in the eyes of others. When power, especially military force, is used, the world will consider it legitimate only when convinced that it is being used for the right purpose - for broadly shared aims - in accordance with broadly accepted norms.

No community anywhere suffers from too much rule of law; many do suffer from too little - and the international community is among them. This we must change.

The US has given the world an example of a democracy in which everyone, including the most powerful, is subject to legal restraint. Its current moment of world supremacy gives it a priceless opportunity to entrench the same principles at the global level.

As Harry Truman said, "We all have to recognise, no matter how great our strength, that we must deny ourselves the licence to do always as we please."

A Deluded Scientist

 
The Language of God: A Scientist Presents Evidence for Belief, by Francis S. Collins, Free Press, New York (2006)

Francis Collins is the co-discoverer of the cystic fibrosis gene and the head of the Human Genome Project. His scientific credentials are impeccable. Collins is also a deeply religious man and he writes this book to explain why "... there is no conflict in being a religious scientist and a person who believes in a God who takes a personal interest in each one of us." (p. 6)

Collins claims he was an atheist when he finished his Ph.D. After enrolling in Medical School he began to encounter patients in North Carolina who asked him about his beliefs. He realized that rationalism wasn't working for him; "... if I could no longer rely on the robustness of my atheism position, would I have to take responsibility for actions that I would prefer to leave unscrutinized? Was I responsible to someone other than myself? The question was now too pressing to avoid."

Like so many others, Collins found his answers in the writings of C.S. Lewis. The result was a conversion to belief in God. But which God? This struggle took another year. The tipping point was the sight of a frozen waterfall in the Cascade Mountains.
As I rounded the corner and saw a beautiful and unexpected frozen waterfall, hundreds of feet high, I knew the search was over. The next morning, I knelt in the dewy grass as the sun rose and surrendered to Jesus Christ. (p. 225)
The language is important. The struggle that faces all of us is a struggle between rationalism and superstition. It's tough to be an atheist and it's easy to lapse into superstition, where you give up the fight and let others do your thinking for you. That's why "surrendering" is such an appropriate description of the event. I admire Collins for being so honest.

However, in spite of the fact that he threw in the towel in the struggle to remain rational, he tries to defend his decision in a logical way. According to Collins, there are two powerful arguments in favor of God. Both of them come from a series of apologetic books by C.S.Lewis—better known as the writer of another fantasy series, The Chronicles of Narnia.

The Moral Law refers to the idea that every human being possesses the same concept of right and wrong. It's built into our psyche and there's no explanation for this other than it was put there by God. (I'm not making this up!) Most rational beings would ask questions like; what are those universal laws?; what's the evidence that everyone shares them?; could they be memes?; etc. But once you've abandoned rationality in favor of superstition, these questions are no longer raised. Collins finds the Moral Law extremely persuasive and he doesn't recognize that it's existence is a scientific question.

Is this Moral Law a rational argument for God? It is according to Collins.
Encountering this argument at age twenty-six, I was stunned by its logic. Here, hiding in my heart as familiar as anything in daily experience, but now emerging for the first time as a clarifying principle, this Moral Law shone its bright white light into the recesses of my childish atheism, and demanded a serious consideration of its origin. Was this God looking back at me?
The second persuasive argument is the presence in all of us of a God-shaped vacuum. What the heck is that, you might ask? C.S. Lewis supplies the answer. It's the sensation of longing for something greater than ourselves. It's the "joy" you feel when you read a good poem, listen to Beethoven, or view the beauty of nature. The emptiness we are all supposed to feel cries out for an explanation, "Why do we have a 'God-shaped' vacuum in our hearts and minds unless it is meant to be filled?" (p. 38)

Apparently, there is no conflict between being a scientist and believing in such silly nonsense. Apparently, scientists don't have to ask the hard questions like, does everyone really feel this longing? Do Buddhists in China feel it? Do atheists lead miserable lives because they can never fill the void in their hearts?

What about miracles? To his credit, Collins faces up to the problem in a section titled, "How Can a Rational Person Believe in Miracles." A miracle is an event that "appears to be inexplicable by the laws of nature and so is held to be supernatural in origin." (p. 48) In other words, miracles conflict with science. But do they conflict with rationalism? Let's see if we get an answer from someone who has surrendered to superstition.

According to Francis Collins, you can assess the probability of a miracle using Bayes Theorem. This is a way of calculating the probability of an event given some "prior" knowledge. How does that help? Here it is in his own words.

Assume that you witness a patient who recovers from a "fatal"cancer. Is it a miracle, or is it a rare spontaneous remission?
This is, or course, where reasonable people will disagree, sometimes noisily. For the committed materialist, no allowance can be permitted for the possibility of miracles in the first place (his "prior" will be zero), and therefore even an extremely unusual cure of cancer will be discounted as evidence of the miraculous, and will instead be chalked up to the fact that rare events will occasionally occur within the natural world. The believer in the existence of God, however, may after examining the evidence conclude that no such cure should have occurred by any natural process, and having once admitted that the prior probability of a miracle, while quite small, is not quite zero, will carry out his own (very informal) Bayesian calculation to conclude that a miracle is more likely than not.

All of this simply goes to say that a discussion about the miraculous quickly devolves to an argument about whether or not one is willing to consider any possibility whatsoever of the supernatural.
So, to answer the question, how does a rational person believe in miracles? By admitting that they are possible and evaluating the evidence based on this prior assumption. Cute, eh? It's called "begging the question"—at least it used to be called that before the phrase acquired a new, very literal, meaning. In the world of the theist, it is rational to assume the answer to the question you're trying to answer in the first place. What a funny world.

Chapter Three is a defense of the compatibility of the Big Bang with the Biblical story of creation and of the fine tuning argument as an argument for the existence of God. Time to move along, there's nothing new here. Other chapters are devoted to explaining evolution and human genomes. These are followed by the mandatory criticisms of Young Earth Creationism, and Intelligent Design Creationism.

The interesting part of the book comes in Chapter Ten. This is where Collins explains Theistic Evolution and why it's rational to accept evolution but still believe in a active personal God who can perform miracles, create the universe, and answer prayers. According to Collins, God choose evolution as a way of creating a species who would be intelligent, know right from wrong, and want to worship their Creator. Collins says, "This view is entirely compatible with everything that science teaches us about the natural world" (p. 201).

Not so. The science that I know says there's no obvious purpose or direction to evolution. There is nothing in science to suggest that we are special. and there's nothing to suggest that evolution was designed by a supernatural being. There's no scientific evidence to indicate that humans have a longing or desire to worship the Christian God. To argue that Theistic Evolution is "compatible" with science is a misuse of the word "compatible." You might just as well argue that astrology is compatible with science simply because we can't prove that everything about astrology is definitely false.

As it turns out, Collins doesn't like the term "Theistic Evolution." He proposes that we replace it with "BioLogos" from the Greek "bios" (life) and "logos" (word). The new word, BioLogos, "expresses the belief that God is the source of all life and that life expresses the will of God" (p. 203). I don't think it's going to catch on.

This is a disappointing book. I expected much better from Francis Collins. He has not presented any evidence for belief that we haven't heard before from C.S. Lewis. Moreover, this "evidence" (Moral Law, longing for God) has been refuted half a century ago. Neither a universal Moral Law nor a universal longing for God are compatible with what we currently know about human societies. The conflict between science and religion still exists.

In the end, the only argument that Collins has is the same old last refuge of the superstitious, "Science is not the only way of knowing. The spiritual worldview provides another way of finding truth" (p. 229). This is only satisfying to those who have already surrendered to superstition and made up their minds that the touchy-feely world of human emotions is a valid way of discovering the truth. Those people are seriously deluded.

Ancient Roman Unearthed In London

 
When PZ Myers and I visited London in October, I took him to the cafeteria in the crypt of Saint Martin-in-the-Fields. We ate our lunch on top of the tombs of medieval Londoners. There was a lot of construction going on behind the church.

According to CNN, workers have uncovered a Roman sarcophagus dating to 410 AD. It would be interesting to find out whether this Roman was related to modern Britons. It should be easy to extract DNA and do the test.

Traffic in London is chaotic, especially around Trafalger Square where St. Martin-in-the-Fields is located. If it turned out that modern Londoners were related to Italians it would explain a lot.

More seriously, we need to have better data on the genetics of populations and any DNA samples from ancestors would help. What percentage of genes in modern Britons comes from Romans, Saxon, Jutes, Celts, Normans, or the rest of France?

Sunday, December 10, 2006

Canadian Black Squirrels Take Over Washington D.C.

 
Okay, so "taking over" may be a bit of an exaggeration. But according to the Washington Post black squirrels now make up 5-25% of the squirrel population. They are descended from a small number of Canadian black squirrels released about 100 years ago.

Black squirrels are much more common in Toronto than gray squirrels so there's always been speculation about why that is. So far there's no evidence of a selective advantage so it's probably due to random genetic drift. In fact that's what the result in Washington suggests to me. But that's not what the newspaper article says, ...
Scientists say it's a real-life example of natural selection at work, which has rolled on for a century here without much public notice.
The IDiots have jumped all over this one and for once they may be partly right.


Denyse O'Learly criticizes the article in The Washington Post Thinks It Has Discovered Natural Selection. I agree with Denyse that this is probably not natural selection. It's a clear and wonderful example of evolution—because allele frequencies in the squirrel population are changing—but the mechanism is probably random genetic drift.

I wish people would understand the difference between evolution and natural selection. If you are a pluralist, you recongize several different mechanisms of evolution and natural selection is only one of them. That's why pluralists (i.e. most evolutionary biologists) are not Ultra-Darwinians.

[The photo is borrowed from the definitive website on blackskwerls. Don't go there unless you're prepared to be really, really frightened. The truth about the black squirrel invasion is ....]

There's Way More than One Born Every Minute

 
"There's a sucker born every minute" according to the famous saying incorrectly attributed to P.T. Barnum. Now we have further proof with an announcement by Coca-Cola that the new version of Diet Coke will be fortified with vitamins and minerals begining next Spring. CNNMoney reports that shares of Coca-Cola are up 0.3%, demonstrating that some people know how to profit from suckers.

Skeptical About the "Obesity Epidemic"

 
John Sullum on reasononline reviews two new book on obesity [Lay Off the Fatties]. The books are "Fat Politics: The Real Story Behind America’s Obesity Epidemic" by J. Eric Oliver and "The Diet Myth: Why America’s Obsession With Weight Is Hazardous to Your Health" by Paul Campos. Here's the opening prargraph of an excellent review, ....
The government seems to have made tremendous strides in its War on Fat. In 2004 researchers at the U.S. Centers for Disease Control and Prevention (CDC) said “poor diet and physical inactivity” were killing 400,000 Americans a year, a number that was widely presented as an estimate of “obesity-related deaths.” Just one year later, the estimate had been reduced to about 100,000. To cut the death toll by 75 percent in the space of a year, the anti-fat crusaders must be doing something right.


I'm not a big fan of diet books or any of the lifestyple books that are so common in the bookstores. These two books are probably not much different, but at least they raise an important issue. How much can we trust the headlines? Is there a real problem with obesity in our society?

It turns out that the "reduction" in deaths was entirely due to rational thinking in the face of stupidity. The orignal report of 400,000 deaths per year was as much as the combined total of all deaths due to disease. A bit of common sense prevailed and the Journal of the American Medical Association published a revised estimate of 112,000 deaths per year due to obesity. (Is that a peer-reviewed journal? If so, where were the peer reviewers the first time?)

What about the obesity epidemic? Well, it turns out that part of it is completely artificial. Back in 1985 you were considered obese if your BMI was above 27.5. A couple of years later the threshold was lowered to 25 making millions of American obese overnight. Neat trick, eh?

There's much more,
“Nearly all the warnings about obesity are based on little more than loose statistical conjecture,” says Oliver, adding that there is no plausible biological explanation for most of the asserted causal links between fatness and disease. “The health risks associated with increasing weight are generally small,” says Campos, and “these risks tend to disappear altogether when factors other than weight are taken into account.” For example, “a moderately active larger person is likely to be far healthier than someone who is svelte but sedentary.” Campos cites research finding that obese people “who engage in at least moderate levels of physical activity have around one half the mortality rate of sedentary people who maintain supposedly ideal weight levels.” Lest you think these facts have been noticed only by political scientists and law professors, Campos and Oliver draw heavily on the work of biomedical researchers such as Case Western nutritionist Paul Ernsberger, University of Virginia physiologist Glenn Gaesser (author of the 1996 book Big Fat Lies: The Truth About Your Weight and Your Health), and Steven Blair, the physician/epidemiologist who heads the Dallas-based Cooper Institute.
I don't know if Campos and Oliver are correct but what they say makes sense to me. The whole obesity epidemic nonsense has a bad smell. It doesn't make sense to this skeptic. Here are some examples of distorted science.
Yet none of this contradicts the main scientific point of these two books, which is that the public health establishment, abetted by a credulous and alarmist press, has greatly exaggerated both the strength of the evidence linking fatness to sickness and the level of risk involved. Oliver cites a 2004 New York Times story headlined “Death Rate From Obesity Gains Fast on Smoking,” based on the highly implausible 400,000-death estimate that was later repudiated by the CDC. He also mentions a 2003 A.P. article that announced “Obesity at Age 20 Can Cut Life Span by 13 to 20 Years.” He notes that “the obesity in question was at a BMI of 45 [305 pounds for an average-height man], which affects less than 1 percent of the population.” In a passage that could have been lifted from a critique of U.S. drug policy, Campos says “the basic strategies employed by those who profit from this war are to treat the most extreme cases as typical, to ignore all contrary data, and to recommend ‘solutions’ that actually cause the problem they supposedly address.”
We need more debate on this issue. We need more skeptics.

Are left-handers quicker thinkers than righties?

 
howstuffworks asks Are left-handers quicker thinkers than righties?.

No.

Octopus Skin Invisibility Cloak

 
Looking for a Christmas present for PZ Myers? Look no further. Nature reports that invisibility cloaks made from octopus skin are just around the corner.

P.S. PZ loves Christmas presents. He's only an atheist from January to November.

Saturday, December 09, 2006

Let's Make a Deal! We'll give you Alberta for Minnesota (but only if you throw in Massachusetts as a sweetener)

 
The latest opinion poll in Canada shows the Liberals (red) ahead of the Troglodytes (blue) in every part of Canada except Alberta. Almost 60% of the cowboys would vote for Stephen Harper and the Conservatives.

Alberta was the only major province to prohibit same-sex marriage before they were forced to accept it by the Federal Government. Alberta consistently elects the most right-wing MP's in the country. It's the province that seems least committed to universal health care. They're against gun control, tend to be in favor of capital punishment, and like giving tax breaks to rich people and corporations.

As if that weren't bad enough, they traded Wayne Gretzky to Los Angeles.

I'm pretty sure that Albertans would be happier if they belonged to a country with more cowboys (like in Texas). So here's the deal. We'll give you Alberta and you give us Minnesota. Because there's a lot more oil in Alberta, you'll need to sweeten the pot in order to get rid of Minnesota. Throw in Massachusetts and you've got a deal.

Listen up UK ! We've got an offer you can't refuse

We're willing to give you Alberta. They already have the same Queen as you so that part won't be a problem. Think of the advantages. You'll have your very own cowboys and Charlie can go skiing in Banff instead of Gstaad.

What does Canada want in return? Well, here's the best part ... we'll take Scotland off your hands! How's that for a deal? Scotland would be a perfect fit for Canada. We already have a province that thinks it's a country, and Robbie Burns Day is practically a national hollidy.

Paging Australia

The competition is heating up so this is our last offer. You can have Alberta but we need to get something in return. Not much, mind you, but we can't give it away for free.

It occurs to me that we could kill two birds with one stone. You get the enormous advantage of having a province where everyone loves Crocodile Dundee and you get rid of New Zealand. We'll make a one-for-one swap; New Zealand for Alberta.

Now, I realize the Kiwis have some quaint notions about being an independent country but I don't think that should prevent you from giving it away.

Friday, December 08, 2006

The Three Domain Hypothesis (part 5)

[Part 1][Part 2][Part 3][Part 4]

If the Tree of Life Fell, Would We Recognize the Sound?

I've been summarizing a series of papers that appeared in a recent book, Microbial Phylogeny and Evolution. The underlying theme is the validity of the Three Domain Hypothesis. The Three Domain Hypothesis is the idea that life can be divided into three distinct (monophyletic) domains: archaebacteria, bacteria, and eukaryotes. An important part of the hypothesis is that eukaryotes are descended from ancient archaebacteria.

I've been arguing that the Three Domain Hypothesis has been refuted. It is effectively dead even though most people don't realize it. It continues to be touted in the textbooks in spite of the fact that experts have rejected it as an accurate model of early evolution.

Ford Doolittle has been thinking about molecular evolution for over three decades. Some of you might recall that he was one of the originators of the term "selfish gene." He was a strong supporter of the Introns-Early Hypothesis back in the 1980's but he abandoned it when it was falsified by the accumulation of nasty facts. This is one of the reasons why Ford Doolittle is so highly respected in the community of molecular evolutionists.

As usual, Ford Doolittle offers an insightful analysis of the controversy in his paper "If the Tree of Life Fell, Would We Recognize the Sound?" He points out that different genes give different trees at the deepest level and this is a serious problem. One that can't be ignored. Are there some "hard core" genes that have not been transferred during the exchange phase of evolution, where gene swapping was common? If so, these could reveal the "true" deep phylogeny?

His answer is no. Surprisingly, there are only about 100 genes found in all prokaryotic species. There don't appear to be any standard subset that are more reliable than others. All genes are candidates for orthologous replacement by gene transfer from another species. Doolittle makes the obvious, but often ignored, point that you can only determine if a gene has been exchanged when you have a true phylogeny to compare it with. You can't just assume that your favorite genes reveal the true phylogeny and all others conflicting with it are artifacts of lateral gene transfer. This is what disciples of the Three Domain Hypothesis often do. It's called begging the question.

Doolittle thinks this is bad science ...
There may be a real catch-22 in assessing how much LGT as orthologoous replacement afflicts the core at depth, but given that we know that orthologous replacement can happen and that rampant LGT drives genome (gene content) evolution at the strain-in-a-species level, there is no justification in retaining vertical descent as the null hypothesis and requiring stronger proof for LGT. Rather (at least with greater fairness), we might recast the notion of the existence of a stable core as a hypothesis that needs to be tested, not a truth that needs further elaboration. If the hypothesis is that there is a cadre of genes that have never been exchanged (and that thus track organismal phylogeny), and the test of it requires that there indeed be such universally shared genes that show the same phylogeny, then this hypothesis has yet to be proven.
What about the "complexity hypothesis?" This hypothesis refers to a core of genes that have never been transferred from one species to another because they are all part of a large complex. Presumably, the pieces of this complex are not interchangeable so new genes cannot be accepted. Thus, this core represents the true phylogeny of the lineage and all other genes have been acquired later.

The "true" core, according to this argument, is the complex of genes that are involved in translation. This includes ribosomal RNA and ribosomal protein genes.

There are three arguments against the complexity hypothesis. First, genes for some key translational components do not agree with the ribosomal RNA tree, refuting the idea that all genes of the complex evolved together.

Second, Doolittle points out that the logic is flawed. For example, the parts of ribosomal RNA that interact with ribosomal proteins are highly conserved so there is very little difference between species. The parts that don't interact are quite variable and those are the very parts that determine the phylogeny. Lateral gene transfer of ribosomal RNA genes from one species to another wouldn't have much effect since the only parts that differ are the parts the aren't necessary.

Thirdly, "One might suggest, only half facetiously, that the (still to be determined) congruence of their phylogenies does not mean that they have never been transferred but, radically otherwise, that they have always been transferred together."

The idea here is that the logic of the arguments made by Three Domain supporters does not stand up to close scrutiny. It seems superficially reasonable but falls apart when you poke at it. This is the same phenomenon that we witnessed with the Introns-Early Hypothesis. Clearly, Doolittle has been sensitized by his experience in that controversy. (Alternative splicing is another example of bad logic. We'll poke at that one some other time.)

So what is the alternative to the Three Domain Hypothesis? Doolittle says, "We claim that there are no data to contracdict the possibility that every gene we find in any genome today has experienced at least one between-species LGT in the 3-4 billion years since life began." This means there is no single tree of life and eukaryotes and not closer to archaebacteria than to bacteria. The way to represent early evolution is as a complex Web of Life.

Perhaps there is a plurality (most favored) pattern, or one tracked by several genes that we consider important, but this has yet to be proven. In any case, there is no compelling reason why this plurality pattern needs to correspond, by any simple mapping, to the tree of speciations and cell divisions. We cannot infer a unique tree of organisms from the pattern of relationships among genomes without making further assumptions about evolutionary processes that are just that: still-unproven assumptions. We have, for several decades, thought that our job was to uncover the structure of a Tree of Life, whose reality we did not question. But really, what we have been doing is testing Darwin's hypothesis that a tree is the appropriate representation of life's history, back to the beginning. Like any hypothesis, it could be false.


The figure below is taken from Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American





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

Jan Sapp The Bacterium’s Place in Nature

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

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

Carl Woese Evolving Biological Organization.

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

William Martin Woe Is the Tree of Life.

Radhey Gupta Molecular Sequences and the Early History of Life.

C. G. Kurland Paradigm Lost.






How to Tell the Difference Between Kooks and Mavericks

The latest (Dec. 9, 2006) issue of New Scientist has a remarkably stupid series of articles written by so-called "lone voices." Who are these "lone voices" and why do they get a soapbox in New Scientist? Here's what the editors say, ...
Science works by consensus, right? Well, not entirely. Throughout the history of scientific endeavour there has been a scattering of people who, for good or ill, have swum against the tide.

In this special series of premium articles, we look at these lone voices and what they have brought to our understanding of the world. Harry Collins (see How we know what we know) and Bob Park (see Watch out for the UFOs) start by offering their ideas on how to distinguish true genius from the ravings of a crank.

We then speak to five people who represent very different kinds of outsider: a star who led the pack (David Deutsch, free feature: At play in the multiverse); a non-scientist making bigger waves than the professionals (Jane Elliott, An unforgettable lesson); an experimentalist who put his own health on the line to get heard (Barry Marshall, Hard to swallow); a scientist doing respected work in the context of unlikely beliefs (John Baumgardner, God said, let the dry land appear…); and a genius who is causing a stir outside his original field (Brian Josephson, Take nobody's world for it).

Each offers a unique challenge to the scientific status quo. Can we afford to be without any of them?
The answer to that one is easy. Yes, we can afford to be without some of them; notably, the Young Earth Creationist (YEC) John Baumgardner.

There's a big difference between "lone voices," or mavericks, and kooks. Kooks are genuine out-to-lunch, delusional pseudoscientists who should be ignored. It's easy to recognize kooks because their ideas conflict with fundamental, well-established principles of science.

Take YEC's for example. They aren't working on the frontiers of science where several different explanations are possible. Instead, they are advocating the overthrow of physics, geology, chemistry, astronomy, and biology because all of these sciences refute the idea that the world is only 10,000 years old. Young Earth Creationism is not a clever idea that the scientific establishment is suppressing because they might lose their grants. It is a genuine idiotic idea that only the most delusional Christian would believe. It's about as rational as believing that the moon landings were faked.

John Baumgardner is a genuine scientist with a Ph.D. in geophysics but he's still a kook. If New Scientist can't tell the difference between someone who's lost all credibility in the scientific community and someone who takes an unorthodox, but rational, position, then we're in a lot more trouble than I thought.

There have been plenty of mavericks in science as the lead editorial in New Scientist points out ...
TIME was when all scientists were outsiders. Self-funded or backed by a rich benefactor, they pursued their often wild ideas in home-built labs with no one to answer to but themselves. From Nicolaus Copernicus to Charles Darwin, they were so successful that it's hard to imagine what modern science would be like without them.

Their isolated, largely unaccountable ways now seem the antithesis of modern science, with consensus and peer review at its very heart. Yet the "outsider" tradition persists. Think of Alfred Wegener, the father of plate tectonics and, more controversially, of Gaia theorist James Lovelock. Both pursued their theories in the face of strong opposition from their peers.

Such mavericks can be crucial to progress (see Lone Voices), but are they a dying breed?
The concept is valid. There have been genuine maverick scientists who swam against the tide and won over the scientific community after a hard-fought battle. Peter Mitchell, Lynn Margulis, Carl Woese, and Stephen Jay Gould are good examples. Unfortunately, the editors of New Scientist have destroyed what little credibility they had left by picking Charles Dawrin as an example. What were they thinking? Darwin was 100% establishment. Within a couple of years of publishing Origin of Species, the scientific/intellectual community had been converted. He had a good idea, he spoke, they listened.

In discussions like this it's worth keeping in mind that there have been many more mavericks than we can recall. Most of them are very forgettable because they were wrong.

With this issue, New Scientist has shown us that it should be moved from the science section of good bookstores to the supermarket check-out counter.

Swiffer WetJet Kills Dogs!

Friday's Urban Legend from snopes.com

The claim is that Swiffer WetJet contains antifreeze and traces are left when the floor has been cleaned. If dogs lick the floor they will ingest the poison and die.

The claim circulates in a standard email message from a women who says that her dog and two cats died of liver failure because of Swiffer WetJet. This particular urban legend seems to be widely believed.

It is completely false. Nobody seems to have noticed that the product continues to be sold in stores and the company (Proctor & Gamble) has not been bankrupted by massive lawsuits from pet owners.

Thursday, December 07, 2006

Why Kyoto Is Important

The Kyoto Protocols set out goals for industrialized nations to lower carbon dioxide emissions and other pollutants. On average, greenhouse gas emissions should be reduced by about 5% relative to 1990 levels. The Kyoto Protocols came into effect in February 2005. 141 industrialized nations signed on, the only significant countries that didn't ratify the treaty were Australia and the United States.

We all share this planet and it is every one's responsibility to behave in a manner that will make our children proud. The real meaning of Kyoto is not in the goals or whether they will be met. The significance is in the effort and the agreement to cooperate for the common good. Kyoto is a big step forward in international relations and that's why we need to support the effort. Turning your back on Kyoto is like slapping your friend in the face after you have shaken hands on a deal.

Canada has just done that when Stephen Harper announced that we would not try to meet our objective. Will things be any different if the new leader of the Liberal party becomes Prime Minister?


You bet they will!

Stéphane Dion is serious about environmental issues and he will reinstate Canada's commitment to the Kyoto Protocols when he becomes Prime Minister next Spring. This will help restore our credibility in the world.

I'm hoping he will be able to convince the Americans that they should join with other nations in making an effort to improve the planet.

Thanks to James Bowie for getting the photo of Stéphane Dion and his dog "Kyoto."

Same-sex marriage in Canada

Same-sex marriage has been legal in Ontario since June 2003. It gradually spread to other provinces as provincial courts declared that laws prohibiting same-sex marriage were unconstitutional. By June 2005, same-sex marriage was legalized in eight provinces and one territory.

The House of Commons passed The Civil Marriage Act (Bill C-38) on June 28, 2005 by a vote of 158-133. This law made same-sex marriage legal in all of Canada. (Alberta had been the major holdout against same-sex marriage.)

Recently, the new Conservative government of Stephen Harper put a motion to re-open the debate on same-sex marriage. The motion was voted on today and the result is ....



defeat for Harper. MP's voted 175-123 to not re-open the debate. The law stands and same-sex marriage is still legal.

Canada remains on the same side of this issue as most other civilized countries.

Why hasn't America legalized same-sex marriage? Is it because of religion? Is it because the American constitution, and the concept of human rights, is different than all other constitutions?



Don't Mess with Professors!!!

This guy is my hero! One of these days I'm gonna do the same thing when a student talks on the phone in class.

Why Woodpeckers Almost Went Extinct!!!

 

Wednesday, December 06, 2006

Stephen Lewis on AIDS

Tonight on "The Nature of Things with David Suzuki" the entire show was devoted to Stephen Lewis and his tireless battle against AIDS in Africa. Visit the Stephen Lewis Foundation Website for more information on this extraordinary man.

You must watch his final address from the XVI International Conference on AIDS in Toronto, August 2006. Lewis will be leaving his position as UN Special Envoy at the end of December. Let us hope we haven't heard the last of him.

John Wilkins on the Sandwalk

 

John Wilkins of Evolving Thoughts resting in the shelter on the Sandwalk.

What is he reading?

Two Kooks in a Pod

Casey Luskin, the chief IDiot over at Discovery Institute has posted an addendum to his inept article on junk DNA [Follow-up on Junk-DNA]. Luskin has discovered the junkdna.com website of Andras Pellionisz. Those two deserve each other.

More Sandwalk

Photos by Richard Carter.

Nobel Laureates: Hans Fischer

 

The Nobel Prize in Chemistry 1930.

"for his researches into the constitution of haemin and chlorophyll and especially for his synthesis of haemin"

Hans Fischer (1881-1945) determined the structure of "haemin," the prosthetic group in hemoglobin. We now refer to this molecule as heme. (Hemoglobin consists of a protein, globin, and a bound cofactor, heme.) The technical name for heme is Fe(II)-protoporphyrin IX (see figure below). In hemoglobin, oxygen is bound to the central iron atom.

Fischer worked out the structure of the porphyrin rings, a considerable feat in those days. He also discovered that the structure of chlorophyll was similar to that of heme.

Tuesday, December 05, 2006

Charles Darwin Is Coming to Toronto

The Darwin Exhibit is coming to the Royal Ontario Museum (ROM) from March 8 - August 4, 2008! I can hardly wait. Let's have a Howlerfest in July 2008. Save the date.

Creationist Engineer Demonstrates the Meaning of IDiot

Check out 'Looney' - another creationist engineer with all the answers from Scott Page on All-Too-Common Dissent.

On talk.origins there's something called the "Salem Hypothesis" which states that when a creationist claims to understand science they are much more likely to be an engineer than a real scientist.

Excited Molecules

One of our students just gave a seminar on molecular dynamics simulations. She's attempting to model an important biochemical process as part of her thesis project. She showed us the image above from a website on Molecular Dynamics Simulations and I thought I'd share it with the rest of you. It shows the three basic ways in which chemical bonds can vary; they can stretch, they can rotate, and the bond angle can change.

Walk the Sandwalk!

The American Natural History Museum has prepared a short video that lets you Take a Short Video Tour of the Sandwalk. You can walk the path that Darwin walked. If you can't go there in person, this is the next best thing.

Thanks to Colin Purrington for letting me know about this. It was part of the Darwin Exhibit.

If you've walked the Sandwalk, send me a photo. That's PZ Myers on the left.

Physarum

The University of British Columbia (UBC) Botanical Garden publishes a Botany Photo of the Day. Today's photo is Physarum cinareum, a slime mould. Slime molds are important protists—single-cell eukaryotes. A related species Physarum polycephalum is studied in several labs and we are anxiously awaiting the results of the Physarum polycephalum Genome Project.

Back in the 1970's, Physarum was a leading candidate for the protist model organism but it fell out of favor 'cause it was too hard to work with. It's still studied in some labs because of its unusual RNA editing. Unlike all other species, Physarum can edit RNA by inserting new nucleotides and by substituting nucleotides.

Monday, December 04, 2006

See the IDiots Gloat

Dave Scott and Uncommon Descent have "discovered" that the homepage of TalkOrigins Archive has links to porn sites [Talkorigins.org Delisted by Google for Porn Links On Home Page]. It sure didn't take them very long did it?

Naturally, being IDiots, they attribute this to some sort of evil evolutionist conspiracy in spite of the fact that the real explanation has been widely disseminated. Read the comments. Dave Scott openly wonders whether the site was really hacked. Shame on him.

Teaching and New Technology

 

"Academic Matters" is a journal of higher education published by the Ontario Confederation of University Faculty Associations (OCUFA). The Winter 2006 issue contains several articles on a subject that's dear to my heart—the role of new technolgy in university teaching.

I'm old enough to remember when television was going to revolutionize university teaching. Back in the 1960's all new lecture theaters were constructed with multiple TV sets dangling from the ceiling. The new technology was going to change lectures forever. No longer would Professors be standing at the front of the lecture room. Instead, they would prepare their lectures in a TV studio and students would watch them on the small screen. Only the best Professors from all over the world would be giving the introductory lectures in biology and physics.

When I arrived at the University of Toronto in 1978 there was a huge TV studio on the main floor of this building. Two years later it was gone. What happened?

Computers were the new technology. By the end of the 1980's we were teaching students how to access remote databases and how to communicate by email. We set up our first course newsgroup in 1989. A few years later (1995) we created class websites and by 2000 everyone was using powerpoint. Today there are entire courses given electronically (e-learning) and podcasts are all the rage in some circles.

Does any of this improve education? I doubt it. There are still Professors who write on the blackboard and don't know the first thing about Dreamweaver (ugh!) or XML. There's no evidence that students in their class are suffering.

This is the issue that's explored in the latest edition of Academic Matters.
But when all is said and done, how much has information and communications technology changed university life? What has been its effect on faculty and students? Has it made a meaningful difference in the quality and quantity of learning that takes place on campuses?
Heather Kanuka is a Professor at Athabaska University, a school that has specialized in e-learning. She cautions that there is little empirical data to support the grandiose claims of e-learning [Has e-learning delivered on its promise?]. There's no evidence that it is as effective as standard lectures, and there's no evidence that it is even cost-effective. Peter Sawchuck (University of Toronto) cautions us to keep e-learning in its proper place [Curbing our enthusiasm: the underbelly of educational technology.

There are three other articles. They all express skepticism about the claims of the new technology. None of the articles are written by Luddites who don't know how to use the new technology and that's what make them so interesting.