Closed on December 25th

Imagine, my Timmy's is closed on the one day you need it the most.

Merry Christmas Everyone!

Will Santa be Affected by Solar Flares?

An article posted on the Natural Sciences and Engineering Research Council of Canada (NSERC) website has the answer [Santa Claus and Solar Flares]. Learn the size of Santa's sled and how he manages to deliver all the presents.

The Hypocrisy of Scientific American

 
The editors of Scientific American are worried about PLoS ONE, the new online journal of science [Peer Review Is Sooooo Old School. They claim this is a big step backwards since the PLoS ONE articles reportedly circumvent peer review. Scientific American set itself up as the protector of scientific integrity and they vow to uphold these high standards in spite of the fact that the scientific community is letting them down.

This is wrong on so many levels that I hardly know where to begin. The real problem with science education is Scientific American, not PLoS ONE.


Here's what the Scientific American editors say,

With the burden of proof off of the reviewers, we in the science press will have to be more vigilant than ever. We can't rush to put stories out until we've focus- grouped findings with a number of experts in a study's particular field. It will force us to become better reporters and to resist the urge to sensationalize and invoke hyperbole--which, while it may not move magazine units or generate hits, will make our service more noble. We'll put in contingencies in order to avoid situations like the false alarm that plagued Lehigh mathematician Penny Smith--the poor woman who posted a flawed proof of the Navier-Stokes equations this fall on arXiv.

SciAm has already started on this path, by the way, as evidenced by JR Minkel's write-up of this morsel from the journal's inaugural issue: Rest easy, creationists, turns out we're a little less like chimps than we previously thought.

PLoS ONE is opening a possible Pandora's box into a brave new world of publishing that's as terrifying as it is exciting. From this point forth, information going from the lab to the journalist's wire (and then onto the public) will be less and less scrutinized and fact-checked. It's the dissemination of scientific information sped up to the breakneck velocity of the 21st century. Here we go...

Bullshit! This is not the end of peer review. The review of PLoS ONE articles is no different than that of many other scientific journals. I will be very surprised if the quality of papers ends up being any different than those published in Cell, Journal of Biological Chemistry, or Nature. All of these journals publish unadulterated rubbish from time to time and brilliant papers as well. The quality of papers in the leading "peer-reviewed" journals ranges from embarrassing to excellent.

PLoS ONE won't be any different.

I'm very upset by the fact that Scientific American editors see themselves as the guardians of scientific integrity, and I'm flabbergasted that they think they can recognize good science from bad science. Their record over the past few years proves them wrong. They have published all kinds of trash in my field, and probably other fields as well. They have hyped stories that don't deserve to be featured in Scientific American proving that their editors are suckers for press releases and self-promotion [The Alternative Genome, Why Are Some Animals So Smart?, The Real Life of Pseudogenes].

In the recent past, the "vigilance" of Scientific American editors and staff writers has left a great deal to be desired. If this crazy false alarm over PLoS ONE makes them pull up their socks and consult more widely before publishing then that's going to be good for science education.

I'm not holding my breath.

(RPM at Evolgen is also upset with Scientific American: Science Reporters Lament the Advent of PLoS ONE.)

E-Z Answer Squirrel

The E-Z Answer Squirrel will answer your most profound questions about religion, like "Does God hate me because I'm gay?"

Brought to you by the United Church of Canada, a church that understands sarcasm.

You Can Call Me Pope Larry !

Which Historical Lunatic Are You?
From the fecund loins of Rum and Monkey.

In the UK, 63% Are Not Religious

According to a Guardian/ICM poll 63% of the people in Briton are non-religious compared to 33% who describe themselves as religious. The non-religious group includes many who call themselves Christian but presumably don't practice the religion. Most people think that Religion does more harm than good - poll.

It's important for North Americans to understand the differences between us and Europeans. While religion still seems to be a powerful force in America, it is on the wane in most other western industrialized nations. That's a reason for optimism. It's possible that North America will soon abandon religion as well.

Breaking News: the IDiots Don't Understand Neutral Theory

 
DaveScot reveals his ignorance in: The Sound of The Neutral Theory Exploding.

Poor Dave, he doesn't know that there are many examples of synonymous mutations having an effect on protein expression. They've been known for decades. Look up "codon bias" for one such example.

As usual, the IDiots get confused about the difference between exceptions and generalities. They think that every little exception to a general rule invalidates the rule and overturns all of biology. This is why we call them IDiots.

Jason Rosenhouse Reviews Orr's Review of Dawkins

Read it at Orr on Dawkins. Good job, Jason. Orr looks like one of them appeaser scientists who have to bend over backwards to defend religion against atheism. I especially like the argument that it's okay to believe in magic and superstition as long as you couch it in sophisticated, intellectual language.

Don't Forget Somalia

As we ponder what to do in Iraq and Afghanistan we do well to remember our failed attempt to impose democray in Somalia. The fighting is still going on and the United Nations is still making noises about it [UN urges end to Somalia fighting].

Would it have been any better if 50,000 western troops have tried to establish law and order? Was cut-and-run a good strategy for Somalia? I think so, and I think it might be the best strategy for Afghanistan and Iraq as well. Let them sort out their own problems and stop complicating things by giving the people a reason to unite against a common enemy (foreign invaders).

They Closed My Timmy's!

It was three weeks ago today and it was only for one day, but it's taken me this long to get over it.

I got up one Saturday morning and went off to my local Tim Horton's to get coffee and a donut. The store was closed and there were strange looking trucks parked on the road. What was going on? Timmy's are supposed to be open 24/7—they're not allowed to close Tim Horton's, are they?

There were famous-looking people living in the white trailers. Cameras were everywhere. There was even a hearse parked in the drive-through. (Look closely in the photo on the left.

The manager (below right) needed a police escort because of the rioting customers. He gave us all gift certificates but that was small compensation for our tragic loss. They opened up the next day but the damage had been done. I'm told we can see what they were up to by going to the movie theatre next summer. As if I'm going to believe that!

Excellent!

My Peculiar Aristocratic Title is: His Excellency Laurence the Incomplete of Midhoop St Giggleswich Get your Peculiar Aristocratic Title

The White House

 
Friday's Urban Legend

The Canadians soundly trounced the Americans in the War of 1812. One of the goals of the campaign was to demonstrate the ability of the mighty British Empire to deliver shock and awe to the enemy capital. To this end, Washington was invaded and looted in 1814 and the White House was set on fire. The Americans were so intimidated that President Monroe soon surrendered.

This is all well-known historical fact. Something that Canadian and British schoolchildren learn in history classes when they are 10 years old.

The name "White House" is thought to be derived from the whitewash that Americans put on the house when the fire damage was repaired. It seemed to have been part of a larger campaign to whitewash everything that had to do with losing of the War of 1812.

That part is urban myth according to snopes.com [White House Wash]. The President's house was known as the White House before the War of 1812 and the original house, built in 1798, was whitewashed.

Skeptical Climatologists

 
Kevin Vranes of No Se Nada writes about impressions he got from a recent meeting of geophysicists [So what happened at AGU last week?]. Apparently, some climatologists are worried that they may have oversold climate change and supressed legtimate skepticism over some of the details.

This is a very important issue in science. It does not mean that warnings about climate change are totally wrong or misguided. What it means is that contrary opinions within the scientific community aren't getting attention for fear of diluting the important message that the public needs to hear.

It's an issue in other disciplines as well, such as evolutionary biology. Skepticism, which is the essence of science, doesn't play very well in the public arena. Scientists who are skeptical about some aspects of evolutionary biology are sometimes considered to be traitors to the cause of defeating creationism. I imagine that the same sort of thing might be happening in the field of climate change.

Varsity Centre Bubble Now Inflated

 
The new Varsity Centre bubble has now been inflated over the University of Toronto football field on Bloor Street. Students have been looking forward to this event for some time: it means they can now play Ultimate Frisbee all winter.

The press release talks exclusively about athletics but we all know the real reason for creating such a large, heated enclosure. In Canada, the gyms and arenas are stuffed with desks and chairs at this time of year and used for exams.

Rumor has it that the bubble is energy efficient. It recycles a lot of the hot air generated on campus.

Mammalian Gene Families: Humans and Chimps Differ by 6%

The first issue of PLoS ONE has just been published. PloS ONE publishes peer-reviewed, open-access, articles that are freely available on the internet. The journal is supported by the Public Library of Science (PloS), a non-profit organization.

The article that I've been waiting to see is,

Demuth, J.P., De Bie, T., Stajich, J.E., Cristianini, N., and Hahn, M.W. (2006) The Evolution of Mammalian Gene Families

Demuth et al. examined gene families in five species whose genomes have been sequenced (human, chimpanzee, mouse, rat, dog). Gene families are normally defined as groups of related genes having more than one copy in a genome. For example, the globin gene family consists of multiple copies of related globin genes such as myoglobin, α-globin, β-globin, and others. The authors appear to use a different definition, which counts orthologous genes in different species as a gene family. Thus, their paper discusses "gene families" that have single genes in different species.

By scanning the available genome sequences, Demuth et al. were able to cluster all genes into 15,389 groups called "gene families." Of these, 3,114 were single genes confined to a single species. These were presumed to be annotation artifacts and were discarded. Not all of the remaining groups were present in all five species. A total of 2,285 additional groups were confined to distinct lineages on the mammalian tree indicating that they had been "created" after divergence from the common ancestor. This leaves 9,990 groups that were probably present in the ancestor of dog, human, chimp, mouse, and rat.

The question is, how many of these gene families show gain or loss of numbers during mammalian evolution? The answer is 5,622 or 56.3% (5622/9,990). The data is shown in Figure 1 (below). The red section of the pie chart represents groups that have experienced a reduction in the number of members of a gene family (or loss of the entire group) in a particular lineage. The green section represents a gain in the number of genes in a family.

Figure 1. Distribution of gene gain and loss among mammalian lineages.

Creative Commons Attribution License

If we focus on the human/chimp comparison, it turns out that the human genome contains 1,418 genes that do not have orthologs in the chimpanzee genome. What this means is that if we look at the identical sections of human and chimp chromosomes one of them will have a gene that the other one does not have at that position. It turns out that the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans. If there are 22,000 genes in the genome, then this total of 1,418 differences represents 6.4% of the genes.

It's important to note that this does not mean that entirely new genes are created or destroyed. What it means is that there have been duplication events such that a gene has been duplicated in one of the lineages. For example, let's say that the region of the chromosome containing the α-globin genes was duplicated in the chimpanzee lineage. This would count as a gain in chimps relative to humans.

There are several problems with the analysis. One of the most severe is the lack of complete coverage of the chimp genome and the relatively poor annotation compared to the human genome. Only 94% of the chimp genome is available while the human genome is about 99% complete and much more accurate. This means that there will be a number of genes in humans that won't appear in chimps. It's unlikely that these problems lead to errors of more than 2-fold.

The authors are clearly aware of the fact that most of these changes in gene number have no effect on the organism. They are accidental changes due to random genetic drift. They are also aware of the fact that some of the duplications and losses are variants that are segregating in the human and chimp populations. In other words, they are not fixed differences.

Nevertheless, Demuth et al. point out that some of the gains and losses of genes could be responsible for the phenotypic differences between chimpanzees and humans. They caution us that the traditional 1% difference in the sequences of orthologous genes may not be the whole story.

An Example of High School Biochemistry

 
I don't know exactly what to make of this. It is not exactly correct, but it's not exactly wrong, either. I wonder what grade produced it?

Grading Exams

 
I've written about the difficulties of grading exams and about the fact that it's almost impossible to get the perfect distribution. We have our tricks. Now, Daniel J. Solove of Concurring Opinions has let the cat out of the bag by revealing one of our most garded secrets—the staircase technique. He spills the beans in A Guide to Grading Exams.

You'd think there ought to be a movement to drum him out of the teacher's union, but no, instead his article is advertised in The 98th Carnival of Education. What is this world coming to?

The Carl Sagan memorial blog-a-thon

 
Carl Sagan died ten years ago today. My contribution to the Carl Sagan memorial blog-a-thon is a quotation from page 297 of The Demon-Haunted World.

Have I ever heard a skeptic wax superior and contemptuous? Certainly. I've even sometimes heard, to my retrospective dismay, that unpleasant tone in my own voice. There are human imperfections on both sides of this issue. Even when it's applied sensitively, scientific skepticism may come across as arrogant, dogmatic, heartless, and dismissive of the feeling and deeply held beliefs of others. And, it must be said, some scientists and dedicated skeptics apply this tool as a blunt instrument, with little finesse. Sometimes it looks as if the skeptical conclusion came first, that contentions were dismissed before, not after, the evidence was examined. All of us cherish our beliefs. They are, to a degree, self-defining. When someone comes along who challenges our beliefs as insufficiently well-based—or who, like Socrates, merely asks embarrassing questions that we haven't thought of, or demonstrates that we've swept key underlying assumptions under the rug—it becomes much more than a search for knowledge. It becomes a personal attack.

Sagan combined skepticism with finesse. That was part of his charm.

The Blasphemy Challenge

 
The IDiots are making a fuss about The Blasphemy Challenge. If you don't know why the IDiots have their knickers in a knot then watch this video from YouTube .

Dissent Isn't Welcome on Uncommon Descent!

 
DaveScot says,

Larry, why do Darwinists insist on calling ID creationism?

I don't know. Why don't you ask a Darwinist?

If you want to ask me why I call your creed Intelligent Design Creationism then feel free to come on over here and ask. I don't ban IDiots. In fact, most science bloggers don't ban IDiots because the IDiots supply much of the comic relief on science blogs.

You’ll need to answer on your own blog because you’re no longer welcome on this one.

Libya Reverts to the Stone Age

 
Several bloggers are all over the this story [Six innocent people sentenced to death.] It concerns five foreign nurses and a doctor who went to Libya in 1999 to help look after sick children. Many of the children became infected with HIV and developed AIDS. Genetic testing has shown that the virus was present before the team of nurses and doctors arrived at the hospital but, in spite of the scientific evidence, the Tripoli Six have been convicted of spreading the disease and sentenced to death.

There has been rejoicing in the street in Libya as citizens demonstrate their support for an ignorant court.

Denyse O'Leary Never Learns

 
Since first meeting Denyse O'Leary a few months ago, we've had several interactions where I attempted to explain why "Darwinism" is not an appropriate synonym for modern evolutionary biology. From time to time she actually seems to get it. She's even agreed to try and be more honest about referring to evolution instead of harping on "Darwinism" as the number one bogey man.

Alas, it didn't last long. Denyse has posted a long diatribe based on some unsubstantiated claim that a professional society is "hassling" a scientist who dares to question Darwin. She says,

Darwinism is their perpetually virgin theory that can never be impugned. Have you noticed how absolute are the claims they make for it? You’d have as much luck discussing science-related questions about Darwin’s theory with them as discussing Mary’s state of grace with Mickey and Ladislaw.

Once again, you're dead wrong Denyse. Lots of us question classic "Darwinism," as did Stephen Jay Gould, the former President of the American Association for the Advancement of Science (AAAS, a professional society). Modern evolutionary theory has moved well beyond what Darwin knew in the nineteenth century. Science is constantly changing—it does not rely on the literal reading of ancient texts. When will you ever learn?

Nobel Laureates: Hans Krebs

 
The Nobel Prize in Medicine 1953.

"for his discovery of the citric acid cycle"

Hans Krebs (1900-1981) received the Nobel Prize for working out the pathway for oxidation of the two carbon acetyl group on acetyl-CoA via a series of tricarboxylic intermediates. The cyclic pathway is now known as the Krebs cycle, the citric acid cycle, or the tricarboxylic acid cycle (TCA cycle).

Krebs had previously been known for his excellent work on the urea cycle in the 1920's and 30's. However, the citric acid cycle was controversial from the beginning. (See Monday's Molecule #6.) By the time he received the Nobel Prize, most biochemists were convinced but there were some hold-outs, making this one of the more controversial awards.

The modern citric acid cycle differs very little from the one published by Krebs over fifty years ago. The main difference is that today we recognize cis-aconitate as an intermediate in the reaction catalyzed by aconitase and not as a separate intermediate in the pathway.

It's Official! Pharyngula Is Best Science Blog!

 
Best Science Blog: Pharyngula

Congratulations PZ Myers!

Michael Denton and Molecular Clocks

It's easy to construct a phylogenetic tree using cytochrome c sequences (left). The tree shows us that bacteria and eukaryotes form two separate branches just as predicted by evolution. Within the eukaryote branch, we see that plants, fungi, and animals form distinct groups. Again, this is exactly what evolution predicted.

One of the remarkable things about these trees is that the branches have similar lengths. Beginning at the base of the tree, the distance to plants, animals, fungi, and bacteria is about the same. It differs by a factor of two, at most, for any species. This is evidence of a molecular clock—a roughly constant rate of evolutionary change for every lineage over a period of hundreds of millions of years. (Cytochrome c is not the ideal sequence for showing this since it's pretty small as far as proteins go. Substitutions of only a few amino acids can make a big difference to branch lengths. Larger proteins show more regular molecular clocks.)

We know why there's a molecular clock. It's because the vast majority of changes in the amino acid sequences of proteins are due to fixation of neutral, or nearly neutral, mutations by random genetic drift. As with any stochastic process, the law of large numbers produces a predictable pattern. In this case, a relatively constant rate of change over hundreds of millions of years.

As it turns out, the overall rate of fixation of neutral alleles should be close to the mutation rate. This is a conclusion derived from population genetics models and those models are well supported by evidence. Since mutation rates are similar, if not identical, between species this rate becomes roughly constant in each lineage. The branch lengths in the cytochrome c tree reflect this indirectly since they result from a combination of fixation times and mutation rates. Furthermore, they are amino acid sequences so a lot of the underlying mutations at the nucleotide level are hidden.

Michael Denton knows of this population genetics explanation since he mentions it on page 289 of Nature's Destiny: How the Laws of Biology Reveal Purpose in the Universe.

Comparisons of these two rates, the rate of mutation and the evolutionary substitution rate, have revealed the very surprising fact that the two rates are the same. This remarkable finding that the difference between the DNA sequences of different species have been generated by mutation and that other factors such as natural selection could only have played a relatively minor role.

Denton knows that the data supports such an idea because he brings up cytochrome c on the next page.

By comparing sequences a curious pattern was observed. For example, in the case of cytochromes, all the higher organism cytochromes (yeasts, plants, insects, mammals, birds, etc.) exhibit an almost equal degree of sequence divergence from the bacterial cytochrome in Rhodospirillum. This means that all their cytochrome genes have changed to about the same degree—in other words, have evolved at a uniform rate.

The uniform rate of change is what impresses Michael Denton. As I mentioned above, Denton knows that adaptation (selection) is ruled out as an explanation. Unlike many other IDiots, Denton knows that pan-adaptationism (often called Darwinism) is not the prevailing view in evolutionary biology.

Random genetic drift is a perfectly reasonable explanation of the molecular clock but Denton rejects that explanation. He says that,

Explanations of uniform rates of evolution in protein genes in terms of genetic drift of neutral mutations fare no better. The rate of genetic drift in a population is determined by the mutation rate. This is not controversial. Although mutation rates for many organisms are somewhat similar per generation time—10^-6/gene/generation—the problem is that generation times are vastly different, so that the rate of mutation per year in, say, yeast, may be 100,000 times greater than a tree or a mammal such as man or elephant, organisms that have long generation times. (p. 291)

The generation time argument is a bit bogus for several reasons. First, mutation rates are based on changes per cell division (replication) and not generation time. Thus, in mammals such a mouse, there are about 50 cell divisions between zygote and gamete and the organism reproduces in about 100 days. Thus, there is, on average, one mutation-causing replication event every two days. This is no more than the average "generation time" of single-celled organisms such as yeast or bacteria. (Bacteria divide once every few days, at most, contrary to what most people believe.)

The second reason for skepticism is that for most of the history of life the "generation time" of different organisms isn't that much different. Large terrestrial mammals, for example, have only been around for about 15% of the time since single-celled life began.

Molecular biologists and population geneticists have thought about these things. They conclude that the evidence favors the idea that phylogenetic trees are due to fixation of nearly neutral alleles by random genetic drift. This explains the molecular clock.

Denton doesn't buy it. He thinks the molecular clock proves Intelligent Design Creationism.

These twin discoveries—that the mutation rate equals the evolutionary substitution rate, and that the rate of change in many genes is regulated by a clock which seems to tick simultaneously in all branches of the tree of life—may represent the first evidence, albeit indirect, that the mutational processes that are changing the DNA sequences of living things over time are indeed directed by some as yet unknown mechanism, or more likely mechanisms. Of course, these discoveries do not prove directed evolution, but it is far easier to imagine them as the outcome of some sort of direction than the outcome of purely random processes. (p. 292)

In other words, Michael Denton can't imagine how stochastic evolutionary processes might work, so God did it. Another argument from ignorance, albeit an ignorance that's on a much higher level than the ignorance usually on display on creationist websites and blogs. (Michael Denton is by far, the most knowledgeable IDiot when it comes to understanding evolution and molecular biology. Perhaps it's why he's out of favor with the true IDiots.)

Junk DNA Disproves Intelligent Design Creationism

 
Micheal Denton explains it in Nature's Destiny on page 289.

If it is true that a vast amount of DNA in higher organisms is in fact junk, then this would indeed pose a very serous challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary events, when it would not in a strict sense be junk in any case, could the finding be reconciled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. On any teleological model of evolution, most, perhaps all, the DNA in the genomes of higher organisms should have some functions.

Sorry Michael, it is true. The genomes of many complex multicellular organisms have vast quantities of DNA that serves no purpose. It's junk. The whole argument of your book just collapsed, as did any argument for intelligent design.

The fact of junk DNA disproves intelligent design and discredits strict Darwinism as well. The IDiots lose twice. Their strawman version of evolutionary biology is wrong and so is design by God.

FLASH! Dembski Will be Paid for his Expert Advice in Dover

 
I'm not making this up. Denyse O'Leary announces that the Thomas More Law Center will pay Bill Dembski for over 100 hours of expert advice on the Kitzmiller case in Dover PA.

Discerning readers might recall that this is the case where the IDiots were blown out of the water. Not a single one of their points was accepted by the judge. I wonder what the going rate is for IDiotic experts?

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.