Odd Sign on Campus

A sign posted all over campus today:

REMEMBER KRAKATOA

August 26, 1883

That’s all the signs say! Is this a public service project from our civil engineering and geosciences department?

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Interesting Molecular Structures

Two cool (or hot) chemical structures today:

Chavicine
Chavicine
Capsaicin

(I’m testing image uploads, and why not test with something interesting.)
Everyone knows that Capsaicin is the hot stuff in chili peppers. Fewer people know that Chavicine is the hot stuff in black pepper. Chavicine slowly isomerizes into piperine, which is less pungent.

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Archaology and open source

The members of the Arc-Team (five archaeologists) run Debian and some other GNU/Linux distributions on three PCs and five notebooks (our whole system). We’ve installed Grass-GIS, different CADs, some applications for virtual reconstruction, statistics, GPS and survey data management, databases (MySQL), etc. We use it primarily because we’re trying to introduce Open Source OS and Open Source applications to the archaeological research. Besides we want to spread the philosophy of free software and free data exchange. In short, why do we use Debian? Because we want to be free!
Find Archaology and open source at: http://www.arc-team.com/

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NYT series on Intelligent Design

I’ve tried to like the science reporting in the times on the ID controversy, but I just can’t. This third article was OK, but reading the first two was like listening to fingernails on a blackboard. I wish journalists didn’t feel it was necessary to provide “both sides” of a debate even when one side of the debate is pretty clearly incorrect. That’s not the biggest problem with the articles, however. The biggest problem is that the debate is stated incorrectly. Kenneth Chang wrote this as the first paragraph of his article:

At the heart of the debate over intelligent design is this question: Can a scientific explanation of the history of life include the actions of an unseen higher being?

The debate actually has nothing to do with scientific explanations or unseen higher beings. The debate is about whether or not we teach patently religious and non-scientific material in science classes. There is no serious scientific debate on Intelligent Design because.., well, because it isn’t science. It doesn’t really matter if the article goes on to demolish ID (which it doesn’t do as strongly as I would like). That first paragraph is what ruins the whole damned thing.

Similar sentiments about the NYT series can be found at Pharyngula and Cosmic Variance.

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Did the tin phase transition end the Scott expedition?

The Wikipedia entry on tin pest mentions the claim that the 1910 Scott expedition to the South Pole may have been doomed by Tin pest (just as Napoleon’s army was). The Scott party, returning from the pole after discovering that Amundsen had beaten them there, found empty kerosene cans at their first cache. The cans had been soldered with tin. Was it poor quality soldering or did the tin phase transition do them in? Once again, this makes a great story, but is possibly apocryphal. The wikipedia entry goes on to say:

The likely cause of death for Scott’s polar party was some combination of scurvy, gangrene, starvation, dehydration, and hypothermia.

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Edward Tufte and Napoleon’s Buttons

Edward Tufte describes this graphic drawn by Charles Joseph Minard as the “best statistical graphic ever drawn”. Beginning at the Polish-Russian border, the graphic depicts the size of Napoleon’s as the width of a line that shrinks from an initial size of 600,000 in June of 1812 to fewer than 10,000 by early December. Napoleon’s retreat from Moscow has always been blamed on the numbing cold of the Russian winter. I always thought that was enough of an explanation.

This book is changing my mind about that. The title, “Napoleon’s Buttons” brings up the possibly apocryphal explanation that the tin buttons used by the Grande Armée to fasten their uniforms underwent a phase transition in the cold. Below around 13.2 °C shiny metallic (β-tin) changes into white, crumbly α-tin. &#946-tin is silvery-white shiny and has a tetragonal structure, while α-tin has a cubic structure. According to WebElements ,

The conversion was first noted as growths on organ pipes in European cathedrals, where it was thought to be the devils work. This conversion was also speculated to be caused microorganisms and was called “tin plague” or “tin disease”.

Did the tin phase transition cause a massive uniform failure that led to the decimation of Napoleon’s army? Possibly, all though the phase transition is not known to be incredibly speedy (α-tin may have a lower free energy than β-tin, but the free energy barrier between the two phases is large). It does make an interesting hypothesis.

“Napoleon’s Buttons” is divided into 17 chapters, each on a different class of molecule that altered human history. I’m only one chapter in so far, but it looks great!

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Woo Hoo!

Yay! Our Nanoparticle vibrational dynamics paper is up on the J. Phys. Chem. B site. This paper really owes a lot to an anonymous reviewer who pointed something out in the review stage. We spent a long time figuring out how to answer the reviewer’s questions, but the final paper was much stronger because of that process.

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Harry Potter and the recessive allele

I’m sure everyone has seen this by now, but this correspondence in Nature is a great read: Harry Potter and the recessive allele.

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Elliot Sober on the Design Argument

I was just reading this article on the Design Argument contributed to The Blackwell Guide to Philosophy of Religion by Elliot Sober. Here’s a quick two-paragraph quote:

In the continuing conflict (in the United States) between evolutionary biology and creationism, creationists attack evolutionary theory, but never take even the first step toward developing a positive theory of their own. The three-word slogan “God did it” seems to satisfy whatever craving for explanation they may have. Is the sterility of this intellectual tradition a mere accident? Could intelligent design theory be turned into a scientific research program? I am doubtful, but the present point concerns the logic of the design argument, not its future prospects. Creationists sometimes assert that evolutionary theory “cannot explain” this or that finding (e.g., Behe 1996). What they mean is that certain outcomes are very improbable according to the evolutionary hypothesis. Even this more modest claim needs to be scrutinized. However, even if it were true, what would follow about the plausibility of creationism? In a word – nothing.

It isn’t just defenders of the design hypothesis who have fallen into the trap of supposing that there is a probabilistic version of modus tollens. For example, the biologist Richard Dawkins (1986, pp. 144-146) takes up the question of how one should evaluate hypotheses that attempt to explain the origin of life by appeal to strictly mindless natural processes. He says that an acceptable theory of this sort can say that the origin of life on Earth was somewhat improbable, but it cannot go too far. If there are N planets in the universe that are “suitable” locales for life to originate, then an acceptable theory of the origin of life on Earth must say that that event had a probability of at least 1/N. Theories that say that terrestrial life was less probable than this should be rejected. This criterion may look plausible, but I think there is less to it than meets the eye. Suppose only ten lotteries are held in the whole history of the universe and that you have just won one of them. The fact that N=10 does not provide a licence for dismissing any theory about how your lottery worked that says that the probability of your winning was less than 1/10.

For those not conversant in the technical descriptions of logical arguments, modus tollens is an argument that takes this form:

If X then Y
not-Y


not-X

A probabilistic version of modus tollens would take this form:

Pr(Y | X) is high
not-Y


Pr(not-X) is high

where Pr(Y | X) is the conditional probability that Y is true given that X is true. Under modus tollens, if a theory X says that Y is probable, and we learn that in fact Y is not the case, then we should conclude that theory X is probably false.

It is relatively easy to find an example which shows that the probabilistic version of modus tollens is incorrect. Sober gives this example in his paper on Intelligent Design and Probability Reasoning.

It is easy to find counterexamples to this principle. You draw from a deck of cards. You know that if the deck is normal and the draw occurs at random, then the probability is only 1/52 that you’ll obtain the seven of hearts. Suppose you do draw this card. You can’t conclude just from this that it is improbable that the deck is normal and the draw was at random. This example makes it seem obvious that there is no probabilistic analog of modus tollens. However, this feeling of obviousness can fade when we look at other examples in which the relevant probability is far less than 1/52.

I’ve seen good scientists fall into the probabilistic modus tollens trap many times. Pointing out the problems with this kind of reasoning is a great defense against the proponents of ID, but honest scientists have to make sure we don’t fall into the same trap ourselves.

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Asymmetric links in random networks and the diameter of the “Blogosphere”

Yesterday’s post had some discussion about complex, scale-free network theory. Since I posted that, I’ve been wondering about network theory as it relates to the blogging community. By now, everyone has seen a “blogroll” list which is essentially a listing of the ideological connectivity of that particular blog (or “node” in the language of network theory). The odd thing about blogrolls is that they are asymmetric links. I may have In the Pipeline in my blogroll, but Derek doesn’t link back to me (at least not yet). So the link between the “OpenScience” and “In the Pipeline” nodes is asymmetric. What I don’t know yet is whether this kind of network has different kind of fragility or robustness under random node removal than networks with symmetric links.

I’ll have to ask László about the robustness or fragility of networks with asymmetric links. Surely someone has worked on this problem, because flow directionality is a pretty important property of highways, railroads, and airlines.

We do know that the “blogosphere” (I hate that word) is probably a scale-free network. There are some blogs (nodes) which are linked by very few others and some which are linked by a nearly infinite number of other blogs (Instapundit and DailyKos come to mind). So the distribution of the number of blogs with a given number of links to it is almost certainly a power-law distribution. For a better description, there a good wikipedia entry on Scale-free networks.

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