December 2006 Archives

China Cabinet

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We finally bought a china cabinet, using money Tiffany’s parents gave us for Winterval.

What I like about the curio is that when we get a full dining room set, with a real china cabinet, we can use the curio for something else, like trophies or artwork.

Tiffany has more on the curio.

PRESS RELEASE—20 DECEMBER 2006 Georgia Citizens for Integrity in Science Education P.O. Box 4642 Marietta, GA 30061 http://www.georgiascience.org/ Email: [Enable javascript to see this email address.] Tel: 770-825-8002 Contact: Professor Sarah L. Pallas, 404-651-1551 (office) or 404-226-4082 (cell)

GCISE APPLAUDS COBB COUNTY BOARD OF EDUCATION

Marietta, GA—Georgia Citizens for Integrity in Science Education (GCISE) commends the action taken by members of the Cobb County Board of Education in dropping any further actions associated with the case Selman et al. vs. Cobb County School District and Cobb County Board of Education. This case resulted from the decision made in 2002 by the School Board to place stickers in science textbooks questioning the status of evolution as a scientific theory.

“The action taken by the Board means that limited resources can be directed to where they have always belonged, in the classroom” said GCISE secretary and Professor Ron Matson. “It further ensures that the Cobb County science curriculum meets the Georgia Performance Standards and that students will understand the central role evolution plays in all biological sciences.”

As an organization dedicated to promoting scientific literacy, GCISE looks forward to working with members of the Board of Education in helping to improve science education throughout Cobb County schools.

Javascripts Return

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I’ve written several custom javascripts over the last few years to do stuff for this blog (and PT). The javascripts were not migrated at the same time that I changed to the new style. They have now returned, after being rewritten to use the Prototype javascript library.

The scripts do the following things:

  • Make links with rel=”external” open links in a new window.
  • Decrypt encrypted email addresses.
  • Using AJAX, quote an existing comment.

Go ahead and play with the last on in comments.

New IP for PT

We’ve switched PT to a new IP address. If your DNS hasn’t picked it up yet, the new ip is 71.170.27.37.

We Won!

I am excited to report that we have won the Cobb Country Disclaimer Case. I’ve been out of the loop, but Ed Brayton has the scoop. Basically, when the 11th circuit appeals court sent the case back to the trial judge for more information, several members of the Dover law team (there is an A-Team parody in there somewhere) joined the case and successfully convinced the trial judge to hold a retrial and allow expert testimony. With the specter of 2 Kitzmiller 2 Furious coming to an Atlanta courtroom, the school district folded. And gave us everything we wanted.

In an agreement announced today, Cobb County school officials state that they will not order the placement of “any stickers, labels, stamps, inscriptions, or other warnings or disclaimers bearing language substantially similar to that used on the sticker that is the subject of this action.” School officials also agreed not to take other actions that would undermine the teaching of evolution in biology classes.

Since I participated in the trial phase and helped organize two amicus briefs for the case, I am excited about this outcome.

What happens when you ignore evolution?

You sentence innocent people to death.

My mother-in-law, Dr. Susan Andrews of Harris County (GA) Schools, was recently announced as the Georgia Superintendent of the Year. This means that for the next year she is the official representative of all the state’s superintendents. This may prove valuable if any Georgia politicians try to monkey with science education this year.

Furthermore, she is also one of the four finalists for National Superintendent of the Year.

Wahaha.

Scambaiting

I ran across this hilarious site for Scambaiters: 419eater.com. Scambaitings occurs when someone responds to a scam email in an effort to use up as much of the scammer’s time as possible. It is funny what the scambaiters can get the scammers to do. Their are stories on the website of scammers posing for embarrassing pictures, joining fake churches, and sending artwork all in an effort to get some “naive” westerner to send them thousands of dollars.

Schelling’s Model

I ran across this interesting blog post on a simple computational model that produces segregated neighborhoods, bit-player: Back to school. It is worth a read.

The sobering lesson of this simple model is that it doesn’t take deep-seated and vitriolic racism to produce a stark pattern of segregation; it’s enough that each of us feels uncomfortable when outnumbered. And the sharp color lines develop even though those who move don’t take race into account when choosing a new location.

I guess I like it because of my interest in geographic genetics and spatially explicit, individual-based models, which is what the third chapter of my dissertation involved.

Squidbillies Rule!

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Squidbilles.gif

Tiffany and I absolutely love Squidbillies; although, she forgets to watch it when I’m not around. Last night’s episode, “Survival of the Dumbest”, was absolutely hilarious. The episode dealt with the origin of squid, with both religious and evolutionary explanations. As usual Early wore various hats, but this time they involved Jesus and Darwin fish.

Probably the funniest moment to me is when the sheriff pasted a warning label on a library book: How Stella—Allegedly—Got Her Groove Back. I was laughing so hard I had to pause my DVR, which I guess happens often with Squidbillies.

In Cobb County the school board would have pasted a wordier disclaimer into the book:

stella-disclaimer.png

Birthday Flowers

Well, Tiffany’s birthday present arrived on time on her birthday. She’s put some photos up on her blog. Go see what I got her.

Good Riddance!

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ellerslie.png

My darling wildernesse has an interesting post up about the removal of her home—unincorporated—town (Ellerslie, GA) from the official state transportation map. You see, the Georgia DOT has decided to remove some 500 location names from their state road map.

Poor Experiment, GA. Poor Dixie Union, GA. Poor Lost Mountain, GA. Poor New Georgia, GA. And poor Reed Creek, GA. They no longer deserve to exist according to the DOT.

As wildernesse points out, the places most affected are either crossroads in rural Georgia or unincorporated communities in the shadow of larger communities, like Evans and Martinez, GA, two suburbs of Augusta.

I have to agree with the man who said it shows a disrespect for the rural areas. Some of those towns are in areas where it’s hard to figure out why it would be cluttered there—Dewy Rose, for instance is near Elberton. There is nothing cluttering up the area near there. Same for Box Springs and Upatoi and Juniper—they are the only things on the map between Columbus and Buena Vista or Butler. How can they be cluttering the map?

Well, actually they are not just taking the nowheresvilles off the map. If you read the names, you realize that they are taking the little towns that are being enveloped by the metro areas off the map. As if Ellerslie, Cataula, Midland, Upatoi, Box Springs, and Mountain Hill were just all one big happy family with its big, dumb neighbor Columbus. I am NOT from Columbus! Why would anyone go somewhere outside a city?—ask Metro-ites. It’s the same for Atlanta—Tucker is leaving too. And Augusta—Evans, Phinizy.

Musella! Pennington! I keep reading names that are real places to me that are being wiped off the map. How are you going to tell people where to get delicious peach ice cream between Forsyth and Talbotton if you can’t point to Musella on the map?

Now that Ellerslie, GA is no longer, I will now have to skip Winterval with the in-laws because I can’t find them on the map.

Go Forth and Vote

The 2006 Weblog Awards

I administrate a group blog on evolution called The Panda’s Thumb. We have been lucky in past elections, with Dover, Kansas, Ohio, and South Carolina coming out on the side of science. Once more our readers need to get out and vote. This time vote for PT for Best Science Blog of 2006.

  • Polls close at 11:59 PM (US - Eastern) December 15, 2006.
  • You may vote once every 24 hours in each poll.
  • After voting in an individual poll you will be locked out from voting again in that poll (on the computer you voted from) for 24 hours.

If you are for puppies and sunshine, vote for Panda’s Thumb. If you like root canals and creationists, vote for the other guys.

Remember, vote early and vote often.

Top 11 Best Geek Gifts

BBspot has a list of the top 11 best geek gifts.

Why am I mentioning it? Well because number 9 involves ID:

9. Simultaneous devolution of all intelligent design proponents into chimpanzees.

It’s nice to see pop culture take swipes at “intelligent design” activists. It helps demonstrate that they are not gaining ground in the “culture wars.”

However, it’s not nice to see pop culture talk about “devolution” and imply that chimpanzees are our ancestors.

And yes, I know that BBspot is not a serious website.

Birthday Surprise

Tiffany’s birthday is tomorrow. I can’t be there to spend it with her, so I’ve sent her a present that will be delivered on her birthday. What it is, I’m not telling.

Well, some minor formatting changes have been made and my latest paper is now available as a provisional PDF from the journal’s website.

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

Here is the abstract:

Background

Studies on the distribution of indel sizes have consistently found that they obey a power law. This finding has lead several scientists to propose that logarithmic gap costs, G(k) = a + c ln k, are more biologically realistic than affine gap costs, G(k) = a + b k, for sequence alignment. Since quick and efficient affine costs are currently the most popular way to globally align sequences, the goal of this paper is to determine whether logarithmic gap costs improve alignment accuracy significantly enough the merit their use over the faster affine gap costs.

Results

A group of simulated sequences pairs were globally aligned using affine, logarithmic, and log-affine gap costs. Alignment accuracy was calculated by comparing resulting alignments to actual alignments of the sequence pairs. Gap costs were then compared based on average alignment accuracy. Log-affine gap costs had the best accuracy, followed closely by affine gap costs, while logarithmic gap costs performed poorly. Subsequently a model was developed to explain the results.

Conclusions

In contrast to initial expectations, logarithmic gap costs produce poor alignments and are actually not implied by the power-law behavior of gap sizes, given typical match and mismatch costs. Furthermore, affine gap costs not only produce accurate alignments but are also good approximations to biologically realistic gap costs. This work provides added confidence for the biological relevance of existing alignment algorithms.

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