September 2006 Archives


Our new couch and coffee table have arrived. Yeah, no more beanbag chairs for me.

Also my PhD diploma arrived this week from UGA; we are going to get it framed to match my BS and AB diplomas.

Georgia and Colorado

Georgia beat Colorado today 14-13 after our backup QB came in and scored two touchdowns in the forth quarter. Colorado looked very good, which I was afraid of coming into this game. Their coach was going to get them to play up to their potential at some point this season, and I was afraid that the Georgia game was going to be the time. I was right. With our defense thinking it was going to have a third straight shutout, we did not focus on the game. At the same time, our new offense hadn’t shown that it was working well together. It showed today, but we pulled out a win, producing the good game that we expected Georgia-Colorodo would be when it was put on the schedule.

Dawg on Nature’s Numbers

I ran across this link today. A blogger called Coalescent was checking out my program, Dawg. He had some problems compiling it, but got it working. I’m not sure what he is doing with it.


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There’s some new stuff coming out in Nature next week on HOTHEAD and maybe a news article in Science as well. I’ll blog on it when it is made public. Here are a couple of earlier posts on the topic:

Existence of RNA Genome or Fertility Selection?


Blog About Hothead and Get an Easy Paper



I got the hardbound copy of my dissertation yesterday. It’s pretty.

Father Coyne in Raleigh

From The News and Observer:

The new priest at St. Raphael the Archangel Roman Catholic Church in North Raleigh is no ordinary clergyman. He’s a scientist, an astronomer and a vocal proponent of evolution.

The Rev. George Coyne, who stepped down as director of the Vatican Observatory last month, will spend a sabbatical on the staff of St. Raphael. He will stay for a year before returning to the observatory in the Arizona desert, where he will continue to lead the Vatican Observatory Foundation.

Cool. The Rev. Coyne may be helpful if creationists try something in NC.

Forget Christmas

Forget Christmas, I’m celebrating “Winterval” this year.

Bible Stories as Fact


Ed has already mentioned that the Texas Freedom Network (TFN) has released its report on teaching the Bible in Texas’s public schools: Reading, Writing, and Religion. The author of the report is a Biblical Studies professor at Southern Methodist University, and he finds—surprise, surprise—that the bible courses offer Sunday school lessons more than they offer actual academic bible study. The teachers (and school districts) are simply not trained in bible scholarship and thus teach their classes from what they’ve learned in Sunday School.

That has always been one of my criticisms of Bible courses. Most districts do not have a teacher trained to know the difference between devotional study of the Bible and academic study of the Bible. Of course, that is exactly the point. Some districts picked teachers because they taught sunday school, while other districts went as far as having preachers come from outside the school system to teach their bible course.

Most of the citizens who push for Bible courses in public schools would probably be horrified to learn what an academic study of the Bible entails. Some people simply don’t like to give equal treatment to different faith traditions of the Bible. And more people don’t like scholarship that doesn’t treat the KJV bible as the completely accurate word of God. These are the types of people that go into fits over the Documentary Hypothesis, which is a must for any serious academic class on the Bible.

I think that students can benefit for an academic study of the bible, but it is nearly impossible to accomplish. Because of the lack of teacher training and the large ratio of bad materials to good materials, it is difficult for a school district to pull it off in a manner that satisfies constitutional and pedagogical concerns. And of course, if a school district happens to pull it off, many of the citizens who want their children in the class will be angered that the children would learns stuff about the Bible in school that contradicts what they learn about it in Church.

As a biologist, a specific worry for me about these courses is that they are often used to push creationism in public schools, which has a long legal history of being unconstitutional. In Finding 11, the TFN’s report states that “Bible courses are used to promote so-called ‘creation science’ and other forms of pseudo-science”. Some courses presented material from Carl Baugh and Kent Hovind as fact, while using their fake credentials to make them sound like authorities.

Brady High School, for example, has followed the suggestions of the NC BCPS and shown a creation science video on Noah’s flood produced by the Creation Evidence Museum in Glen Rose, Texas, an organization that advocates belief in a six-day creation, a 6000-year-old earth, and the coexistence of dinosaurs and humans. It has accepted donations to construct a biosphere intended to replicate the atmospheric conditions prevalent before Noah’s flood. Not content just to show students the Creation Evidence Museum’s video, Brady High School has also hosted Carl Baugh, the founder of the museum, as a guest lecturer. … Brady High School has also apparently followed the NC BCPS recommendation of presenting the well-known and completely discredited urban legend about NASA’ s supposed discovery of a missing day in time as factually accurate. …

In a recent school year, the Forsan High School Bible class spent two days watching the video Dinosaurs and the Bible, produced by Creation Science Evangelism. The course objective for those days is to “show agreement with Biblical record and paleontological discoveries.” An additional day is devoted to a video identified as “Eden and 800-year old men,” which is probably The Garden of Eden, produced by the same company. That day’s objective is characterized as: “Are there possible scientific explanations for long-lived humans in biblical times?” … Approximately half of the questions on a test over “Creation and Genesis Chronology” are devoted to the “young earth” theories of Kent Hovind, founder of Creation Science Evangelism. These include:

According to Dr. Hovind’s thoery an [blank] struck the earth, causing a global flood.

According to Dr. Hovind, fossilization can take place very slowly/quickly. (circle the correct answer)

Give two example of rapid fossilization.

ATDH (according to Dr. Hovind) which of the following can explain fossil stratification (layers) in a flood situation? (circle 4 correct answers) Age/Mobility/tv ads/Body density/Hair color/Intelligence/Habitat

Which of the following is not a proof that dinosaurs live after the Flood?

a. cave paintings by early native Americans

b. dinosaur engravings around Bishop Bell’s tomb at Carlisle cathedral in Britain

c. Barney

d. Bible desription of Leviathan and Behemoth

e. Fossil footprints.

Some districts even taught that Africans, Europeans, and Asians are descended from different sons of Noah, without realizing that such Bible stories presented as fact were used to support racism, slavery, and Jim Crow in the past.

I just hope this report makes districts think hard about what is required to teach an academic bible class in public schools.

Cool Story

This is a cool story. It seems that a red-shirt freshman on Clemson’s football team, Ray Ray McElrathbey, got custody of his 11-year-old brother, Fahmarr, because their parents are addicts. The NCAA has waived some of its restrictions to among other things, allow friends to watch Fahmarr while Ray Ray is at practice and at away games. It cool to see Ray Ray show such maturity, when football players are in the news so much for being immature.

House MD


I agree somewhat with PZ on last night’s House, M.D. As soon as they discovered that the kid had cells with different type of DNA, the obvious answer was chimerism. I suspect that any decent (pre) medical student would have known it right away. Chimerism is something that is included in introductory genetics classes. Of course the viewing public may not be aware of it, which is why TV writers decided that chimerism was the mystery answer.

Another thing missing from the show was the realization that when they ran the DNA, the “mutated” cells had a genotype consistent with that of a sibling.

Speaking of chimeras, I recently ran across this report of a child who was discovered to have one testicle and one ovary.

Strain et al. (1998) A True Hermaphrodite Chimera Resulting from Embryo Amalgamation after in Vitro Fertilization. New England Journal of Medicine 338:166-169. (link)

High rates of successful pregnancy after in vitro fertilization depend on placing more than one embryo into the mother, a practice resulting in a 30-to-35-fold increase in dizygotic-twin deliveries. Increased frequencies of twin-associated anomalies might also therefore be expected. Chimerism, the presence in a single person of cells derived from two or more zygotes, is one such rare anomaly. It is usually ascertained through anomalous blood-grouping results or (for XX/XY chimeras) sex reversal or intersex.

We used DNA polymorphisms to investigate a 46,XX/46,XY hermaphrodite conceived by in vitro fertilization. We found not only that the child is a chimera, but also that he must have resulted from amalgamation of two embryos, each derived from an independent, separately fertilized ovum.

MAC Rules

I guess since I’m at NCSU, I need to pay attention to ACC football (if you can call it that). I am amazed by Chuck Amato’s comments after NCSU lost to a “cupcake” team. Here is ESPN’s report.

“They’re in a conference that allows non-qualifiers in school,” Amato said during his weekly news conference, the Charlotte Observer reported. “Non-qualifiers. Do y’all need to look that one up to write your stories? … Do you know what kind of players non-qualifiers are, usually? They’re inversely proportional to what their grade-point average is. They can make a big difference.”

Translation: We lost because they had better players. Their lower standards gave them an advantage over us.

Wait a second. Which team is a member of a BCS conference? Which team gets to play on national television several times a year? Which team is can count on going to a bowl if they only win half their games? In last year’s NFL draft, which team had six picks, including the number one and two others the first round, while the other only had a single forth round pick?

Sure, high standards hurt the ability of Duke and Vanderbilt to field a competitive football team every year. But, yeah, Chuck is right, those MAC schools get all the advantages. I hope Chuck counts his blessings when he’s coaching the Kent State defense next year.

Holiday Cards for Me

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Glenn Branch just sent me a link to holiday cards—yes holiday cards—that are perfect for me.

Made With Molecules’s DNA Transcription Tree Card

© 2005 Raven Hanna

I think I’m going to order a box.

The Quick Brown Fox

Last night when I was leaving work around two o’clock in the morning, I spotted a gray fox (Urocyon cinereoargenteus) on centennial campus, walking along the sidewalk carrying a mouse in its mouth. I turned my car around and followed it for a couple of blocks. It was funny to watch the fox walk on the sidewalk, cross the street using the cross walk, and continue walking along the sidewalk. I eventually lost it in the parking deck of the RedHat building.

Fastcgi, Movabletype, and Apache

I doubt many of you have noticed that I am now running my blog software using FastCGI. I used the guides here and here to do it.

I modified the dispatch.fcgi code mentioned in the above links because I wanted to use mod_rewrite rules to call the dispatcher. This allowed the same dispatch.fcgi to respond to different requests. The code is at the end of the article.

To get this running, I installed dispatch.fcgi on my server such that it was located at /cgi-bin/mt/dispatch.fcgi. I then added the following lines to my Apache configuration, which allows me to direct any request for an fcgi script in my MT directory to the dispatcher.

    RewriteRule ^/cgi-bin/mt/([^/]+\.fcgi)$ /cgi-bin/mt/dispatch.fcgi/$1 [QSA,L,PT]

    <Location "/cgi-bin/mt">
        AddHandler fcgid-script .fcgi

I’m using mod_fcgid instead of mod_fastcgi to serve the scripts. I’m also working on moving my websites from Apache to lighttpd because of its better support for fastcgi. I’ll still run Apache as a backend to serve requests that lighttpd can’t handle.

Sofa (King We Tard Ed)!

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Tiffany came up to Raleigh last weekend, and we went couch shopping. We ended up buying a couch and coffee table from Carolina Sofa Company. They are made in Asheville will be delivered at the end of the month.

For the couch we went with a red fabric called “airbrush garnet”, with two accent pillows in “ebony replay” and two in “airbrush garnet”. We won’t know how it will look in our townhouse until it is delivered. Until then, I will continue to use the two beanbag chairs Tiffany and I bought when I moved up here.

Fantasy Football

I got talked into playing fantasy football with seven other people from my department. I’ve never done it before, since college ball is much better than pro ball. We had the draft last week, with eight teams making sixteen picks each. I drew the last spot in the draft, which meant I picked eigth and ninth. (We had a zig-zag draft order.) Every week each team must start a QB, two RBs, two WR, a TE, a K, and a Defense. Given that, I put together the following team:

The Dauphins

  • QB C. Palmer (Cin)
  • WR C. Johnson (Cin)
  • WE Sa. Moss (Was)
  • RB E. James (Ari)
  • RB W. Dunn (Atl)
  • TE R. McMichael (Mia)
  • K N. Rackers (Ari)
  • Def Tampa Bay
  • RB R. Bush (NO)
  • WR J. Horn (NO)
  • QB P. Rivers (SD)
  • TE V. Davis (SF)
  • QB M. Vick (Atl)
  • WR R. White (Atl)
  • RB C. Brown (Ten)
  • Def Washington

I’ll try to post updates as the season progresses.

About this Archive

This page is an archive of entries from September 2006 listed from newest to oldest.

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