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.