January 2007 Archives

When Cats Attack

Via PZ, I found this funny discussion of who would win in a battle between a wizard and a cat. Most people in the discussion seem to think that cats are not all that scary or formidable.—They haven’t met our Precious (the torbie in the sidebar).—However, a few weeks ago Tiffany sent me a link to a YouTube video that clearly demonstrates that cats are to be feared.

Mooninites Invade Boston

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After all those reports of a bomb scare in Boston, it turns out that the bombs were actually advertisements for Aqua Teen Hunger Force: Ad campaign triggers bomb scare in Boston. I guess that this is a good reason why first responders need some Continuing Adult Swim Education.

Electronic light boards featuring an adult-cartoon character triggered bomb scares around Boston on Wednesday, spurring authorities to close two bridges and a stretch of the Charles River before determining the devices were harmless.

Turner Broadcasting Co., the parent company of CNN, said the devices contained harmless magnetic lights aimed at promoting the Adult Swim network’s late-night cartoon “Aqua Teen Hunger Force.” Law enforcement sources said the devices displayed one of the Mooninites, outer-space delinquents who appear frequently on the show, greeting visitors with a raised middle finger.

“While the concern is lessened as a result of the investigation, I’d like to remind citizens to treat any suspicious devices with care and to call 911 if any such device is found,” Boston Police Commissioner Ed Davis said.

I hope that this becomes part of a storyline for a future episode of ATHF.

P.S. March 23rd


WTF? It looks like Boston is mad at Turner and have arrested one person:

Peter Berdovsky, 27, a freelance video artist from Arlington, Massachusetts, was facing charges of placing a hoax device in a way that results in panic, as well as one count of disorderly conduct, said Massachusetts Attorney General Martha Coakley. The charge is a felony, she said.

Boston is also looking to arrest more people and file a civil suit against Turner.

I know what Boston needs to do: watch Adult Swim. It’s not Turner’s fault that the Boston government is stupid enough to mistake a marketing campaign for a terrorist plot. Hey, Boston, here is nickel, go buy yourself a clue.

Adult Swim Ad

Adult Swim Ad

Herpes outbreak triggers wrestling ban in Minnesota

An outbreak of a contagious rash called herpes gladiatorum among Minnesota high school wrestlers led the state to suspend matches and halt contact practices, authorities said Wednesday. …

Herpes gladiatorum – commonly known as mat herpes because wrestlers are particularly susceptible – is caused by contact with the same common herpes simplex virus that produces cold sores.

Is it just me or does “Matt Herpes” sound like a 1950’s private eye?

The Oscars

The nominations are out and my three favorite films of the year all got left out: Pan’s Labyrinth, Children of Men, and The Good Shepherd.

Totally Weird

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AP/CNN: ‘12-year-old’ is 29-year-old sex offender

The Yavapai County sheriff’s office also said Neil Havens Rodreick II conned two men he was living with and having sex with into believing he was a young boy. …

Stiffler and Robert James Snow, 43, “were very upset when the detectives told them they had been having a sexual relationship with a 29-year-old man and not a pre-teen boy,” Quayle said. …

She said detectives learned in interviews with the men that Rodreick convinced Stiffler and Snow that he was a boy after they met him two years ago over the Internet. Rodreick apparently shaved his body hair and used makeup to keep up the guise.

You have to wonder why they never figured out that Rodreick wasn’t 12. But I guess asses don’t get five-o-clock shadows.

Tonight Prof. Steve Steve and I went to the North Carolina Museum of Natural Science so that we could finally see Flock of Dodos, Dr. Randy Olson’s documentary about intelligent design’s culture war with evolution. If you missed it, the museum will be showing it several more times in the coming weeks, including on Darwin Day. Many other locations will be showing the documentary on Darwin Day (2/12). Check your local museums and universities. If you can’t get to a screening, Showtime will carry Dodos in May, and stores should have DVDs next fall.

We left work early tonight, around 6:30, so we could brave the bad weather and make it downtown for the 7:00 showing. We got there fine enough, but when we arrived, we discovered that a Dodo was picketing the showing and urging us to repent. Prof. Steve Steve got into an argument with him trying to explain why cell theory and the second law of thermodynamics do not challenge modern biology, but the dodo appeared to have foam in his ears. Eventually, Dr. Olson joined us outside and told us that his movie was about to start. At Dr. Olson’s urging, Prof. Steve Steve and I hurried inside to find some seats and left the Dodo outside arguing with a lamp post.

The museum showed Flock of Dodos on its first floor, in the auditorium, which filled up with some 300 pandas and people . The museum itself is pretty cool, even when not throwing a flock party. It has exhibits demonstrating North Carolina’s natural treasures from the mountains to the sea, with plenty of stuffed animals and shiny rocks. The best part is the third floor’s replica of the Paluxy “man” tracks. Prof. Steve Steve swears that he can totally see where the fossils prove how Adam and Eve and Fred and Wilma chased dinosaurs across the ancient Texas wilderness some 6,000 years ago.

The movie started on time, which was unfortunate since Dr. Olson was trying to say a few words to the crowd beforehand but got cut off by the lights going down and the beginning playing. This was very funny since the first frame of Flock of Dodos is the phrase “Res ipsa loquitur—the thing speaks for itself.”

Throughout the movie, interviews with intelligent design activists were contrasted with interviews with evolutionary scientists, while the shenanigans in Kansas serving as the focal point. The documentary journeys among Boston, Kansas, Pennsylvania, and Seattle. Flock of Dodos provides us with two important points

Dr. Olson answers questions after the talk.

First that the intelligent design movement consists of nothing but lies invented for a public relations campaign and seeks nothing less than the overthrow of the cultural legacies of the enlightenment.

And second that scientists are utterly unable to communicate their profession to normal people, which only helps the crusade of anti-intellectualism.

The later point proves especially provocative in academic settings because scientists don’t like to be told they the lack the tact and social skills needed to reach the people. Not surprisingly, most of the questions that Dr. Olson answered after the showing centered around this issue. It became rather clear that the room agreed with him that scientists need to work on their people skills and learn to actually communicate with people, who may know nothing about science.

I wish he would have gone one step forward and have pointed out that for science to flourish in a democracy, the electorate needs to have a positive understanding of the discipline. Ignorant voters elect ignorant politicians, and science and education suffer as a result. We should educate the masses, not condemn them.

After the official question and answer session, Dr. Olson hung around and took a few more questions from people that walked up to him. Prof. Steve Steve managed to make his way up to the front and took his picture with the filmmaker.—That silly Dodo was nowhere in sight.

And finally, I want to revisit Dr. Olson’s two important points with a question about framing the issue in our favor.

The documentary points out what an effective sound byte “Teach the Controversy” really is. Sure it lacks complete substance, but it is a short rallying cry that easily satisfies the modern requirements of marketing to a populace with a low attention span. We need something similar, not only similar but better, since the scientists in Flock of Dodos were unable to give us one.

So I think this is a good chance to use comments to brainstorm for sound bytes that favor our side of the issue. I’ll start by tossing out two bytes: “What Controversy?” and “Dover Trap”. Go ahead tell me what you think.

The second chapter of my dissertation has now been published. It is freely available from the BMC Bioinformatics website. In this post I hope to provide you will a short overview of the research. The reference is

Cartwright RA (2006) Logarithmic gap costs decrease alignment accuracy. BMC Bioinformatics 7:527.

Our genomes evolve not only via point mutations (where one base changes into another base) but also via insertions and deletions. That is the addition or removal of bases. Collectively insertions and deletions are known as “indels”. Now several studies over the last fifteen years have found that the size of insertions and deletions follows a power law, i.e. a log-log plot of size versus frequency is linear. However, this observation has had little impact on bioinformatics for various reasons. Now why is this observation important? For starters, several scientists have proposed that sequences should be aligned using logarithmic gap costs (wk=a + b k + c ln k) instead of the standard affine gap costs (wk=a + b k).

Because in my first chapter I created a sequence simulation program, Dawg, that could simulate evolution using a power law of indel sizes, I felt that it was important to test this suggestion out. Specifically, whether the slowness of algorithms using logarithmic gap costs are offset by their improved accuracy. So that is exactly what I did for my second chapter, and the results were surprising.

MT Dispatcher Bug Fix


I’ve fixed a bug in my FastCGI dispatcher for Movable Type that would cause it to exit if its calling process had exited. This caused it to end unexpectedly if it had been spawned by spawn-fcgi.

I also added stderr logging and gave the rc.d script some instructions for doing some of the setup for you.

Download Links: The FCGI Server: mt-dispatch (source) The FreeBSD rc.d script: mt-dispatch.sh (source)

Bora of A Blog Around The Clock has edited an anthology of the best fifty posts from science and medical blogs in 2006: The Open Laboratory: The Best Writing on Science Blogs 2006. Several of my friends and colleagues have posts in the anthology. The Panda’s Thumb is represented by Ian Musgrave’s post, Denton vs Squid; the eye as suboptimal design. Several other Pandites are represent their personal blogs in the anthology as well.

You can order yourself a copy of the anthology from Lulu.

Congrats to all the winners.

Evolutionary Parameters

I’m working on a project to estimate evolutionary parameters using an EM algorithm that sums over all possible alignments. I’m working on revising a separate paper and have decided to make a quick estimation of some parameters and use them in some simulations. This is what I got today:

Expected number of substitutions between humans and mice:

0.478222 sub/nuc

Rate of gap formation:

0.213542 gap/sub

Slope parameter for power-law distribution of gap sizes:


These parameters were estimated by comparing the sequences of Intron 7 of Mouse ADH1 gene and Intron 7 of Human ADH1c gene. They give us a clue into the underlying mutational process that has affected the genomes since the species diverged.

This college football season was amazing: from my down and out Dawgs finishing with three straight upsets of ranked teams including a fantastic come-from-behind victory over Virginia Tech in the “Peach” Bowl, to Boise State and Oklahoma giving us the greatest football game in recent memory, and finally to Florida proving every one wrong and taking Ohio State to the wood shed.

Simply amazing.

Florida was lucky this year. They wouldn’t have even been in the championship game if UCLA didn’t beat USC in the last week of the season. Georgia and Auburn weren’t so lucky when they made their runs for the championship in recent years.

In fact, many people believe that Florida didn’t belong in this game, that Michigan should have gotten to plan Ohio State again. Those people were proved wrong when Michigan laid an egg against USC in the Rose Bowl last week. I guess that just shows you that the Big Ten was overrated this year. Ohio State, Michigan, and Wisconsin had great years but in the end none of them beat a top ten team from another conference. In hindsight, their biggest out of conference victories were not over dominant teams: Texas, Notre Dame, and Arkansas.

I guess that just goes to show that once again the SEC is the strongest conference in the land.

This blog has been running Movable Type under FastCGI for several months now, first under Apache and later under Lighttpd. During that time have have written my own FCGI server for MT based on Brad Choate’s original code.

Unlike the original, my version creates several worker threads to handle the blog requests and will reap the workers after they served a certain number of requests. This prevents memory leaks from consuming too much system memory (a problem that I have). Also, unlike the original, my version implements a start_background_task subfunction that is compatible with FCGI. Previously, background tasks would fail FCGI MT installs.

Download Links: The FCGI Server: mt-dispatch (source) The FreeBSD rc.d script: mt-dispatch.sh (source)

Instructions on installing are below the fold.

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This page is an archive of entries from January 2007 listed from newest to oldest.

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