Separating Religion and Medicine

 
Apparently, there's a movement under way to integrate religion and medicine. "Orac" over at Respectful Insolence rips this idea to shreds in Separating doctoring from doctrine.

Mark Twain and the Eiffel Tower

 

A couple of weeks ago, we were watching the final episode of "The Amazing Race" and one of the sites they visited was the Eiffel Tower. It's in Paris, and it made my wife think of going to Paris in the Springtime. That's a great idea but, being somewhat less romantic, I have to admit that my first thought on seeing the Eiffel Tower was "Mark Twain." Huh? Is there a connection between Mark Twain and the Eiffel Tower. Of course there is. There's a connecton between Mark Twain (Samuel Clemens) and everything, if you look hard enough. I thought of him because of this quotation from "Was the World Made for Man?"

Man has been here 32,000 years. That it took a hundred million years to prepare the world for him is proof that that is what it was done for. I suppose it is. I dunno. If the Eiffel tower were now representing the world's age, the skin of paint on the pinnacle-knob at its summit would represent man's share of that age; & anybody would perceive that that skin was what the tower was built for. I reckon they would. I dunno.

Turns out, Mark Twain said many things that are relevant to the debate between rationality and superstution.


Here's a selection from Twainquotes.

Man is the only animal that blushes. Or needs to.

I am the only man living who understands human nature; God has put me in charge of this branch office; when I retire there will be no-one to take my place. I shall keep on doing my duty, for when I get over on the other side, I shall use my influence to have the human race drowned again, and this time drowned good, no omissions, no Ark.

Man is a Religious Animal. He is the only Religious Animal. He is the only animal that has the True Religion--several of them. He is the only animal that loves his neighbor as himself and cuts his throat if his theology isn't straight. He has made a graveyard of the globe in trying his honest best to smooth his brother's path to happiness and heaven....The higher animals have no religion. And we are told that they are going to be left out in the Hereafter. I wonder why? It seems questionable taste.

God's noblest work? Man. Who found it out? Man.

In religion and politics people's beliefs and convictions are in almost every case gotten at second-hand, and without examination, from authorities who have not themselves examined the questions at issue but have taken them at second-hand from other non-examiners, whose opinions about them were not worth a brass farthing.

In the laboratory there are no fustian ranks, no brummagem aristocracies; the domain of Science is a republic, and all its citizens are brothers and equals, its princes of Monaco and its stonemasons of Cromarty meeting, barren of man-made gauds and meretricious decoractions, upon the one majestic level!

Scientists have odious manners, except when you prop up their theory; then you can borrow money off them.

The gods offer no rewards for intellect. There was never one yet that showed any interest in it..

The motto stated a lie. If this nation has ever trusted in God, that time has gone by; for nearly half a century almost its entire trust has been in the Republican party and the dollar--mainly the dollar. I recognize that I am only making an assertion and furnishing no proof; I am sorry, but this is a habit of mine; sorry also that I am not alone in it; everybody seems to have this disease.

What God lacks is convictions- stability of character. He ought to be a Presbyterian or a Catholic or something- not try to be everything.

Molecular Models

 
I often use molecular models to illustrate concepts in my biochemistry class. There are several types of models and the different types can be used for different purposes. For example, I have a big space-filling model of DNA that's very useful for understanding how sequences are read on double-stranded DNA.

I like ball-and-stick models for showing students how flexible small organic molecules can be in solution and for teaching stereochemistry. My favorite model is the Molecular Visions kit sold by a company called Darling Models Inc.

I logged on to the website and charged it to my credit card. The package arrived the following week.

Last night my wife was looking over our credit card statement to see if one of her charges had gone through. She noticed that I had charged $41 to Darling Models Inc.


It took some explaining. I'm still not sure if she believes me. I hope she reads this and follows the link.

Monday's Molecule #6

 
Name this molecule. You must be specific. We need the exact name. Bonus points for explaining why this molecule caused such a controversy in biochemistry. (Hint: it has something to do with the green carbon atoms.) Comments will be blocked for 24 hours. Comments are now open.

See Dunbar's answer in the comments for the correct answer with a good explanation of why Krebbs got in trouble and why his Nobel Prize was questioned by some.

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.

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?

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.

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.