February 2009 Archives

For many years now, I’ve been trying to get the final chapter of my dissertation published. Its gone to several journals, and at Molecular Ecology I finally got a really good editor, who is an expert in the topic. He provided great comments, which finally convinced me to bite the bullet and redo my simulations, updating my analysis.

I’ll post a pre-print when it comes available, but for now here is the abstract information.

Antagonism between Local Dispersal and Self-Incompatibility Systems in a Continuous Plant Population

Reed A. Cartwright

Abstract: Many self-incompatible plant species exist in continuous populations in which individuals disperse locally. Local dispersal of pollen and seeds facilitates inbreeding because pollen pools are likely to contain relatives. Self-incompatibility promotes outbreeding because relatives are likely to carry incompatible alleles. Therefore, populations can experience an antagonism between these forces. In this study, a novel computational model is used to explore the effects of this antagonism on gene flow, allelic diversity, neighborhood sizes, and identity-by-descent. I confirm that this antagonism is sensitive to dispersal levels and linkage. However, the results suggest that there is little to no difference between the effects of gametophytic and sporophytic SI on unlinked loci. More importantly both GSI and SSI affect unlinked loci in a manner similar to obligate outcrossing without mating types. This suggests that the primary evolutionary impact of self-incompatibility systems may be to prevent selfing, and prevention of biparental inbreeding might be a beneficial side effect.

Cluster Magic with LSF

For two of my projects, we’ve been using the HPC cluster at NCSU pretty heavily. This cluster uses LSF for job control and one of the problems we encountered is that several of the worker nodes have scratch directories that are full. Luckily LSF has a solution for that. When submitting jobs, LSF allows you to specify a pre-execution command (bsub -E) that can be used to determine, if a node has the resources to complete a job. If the command is a success, then the job is run on the node, otherwise the job is put back in the queue to wait for another node.

We use the pre-execution command to test whether there is enough space on /scratch to hold our files. For one set of runs, the rule of thumb I use is greater than 1GB of space. Here is our solution:

bsub -E "test `df -B 1G /scratch | grep /scratch | cut -c42-50` -gt 1" [...]

This command works by extracting the freespace on /scratch from df and then comparing it against our limit.

For my second trick, I’ve written my application to respond gracefully to interrupts that ask it to terminate early. When it receives a ctrl-c (INT signal), the program stops cycling, reports partial results, and then exits. This allows the program to be stopped early without wasting the results that it has already gathered. On the cluster, when my jobs have run longer than their time limit, LSF sends a USR2 signal to them, which they treat like the INT signal above.

This was actually not that difficult to implement, the signal function was well documented. However, on the cluster my jobs are contained in a shell script that sets up the environment, calls my application, and then cleans up, moving the output from scratch to a permanent location. This shell script was not handling the USR2 signal gracefully and was thus dieing instead of preforming cleanup. After some digging, I found that I needed to convert my shell script from tcsh (C Shell), which has limited signal handling, to bash (Bourne-again Shell), which has flexible signal handling. Under bash, all I have to do is issue the following command to force bash to ignore USR2 and INT signals.


This allows the shell script to proceed with cleanup after my application has terminated early.

Writing the previous entry reminding me that I never posted the following solution.

While working on my book, The Open Laboratory 2007, I typeset everything in LaTeX. One of the features that I included was a drop cap at the beginning of each entry in the anthology, using the Lettrine package.

However, I could find no way to automate the process in LaTeX, requiring the \lettrine command to be included at the beginning of each entry. This resulted in a few entries missing the drop cap because their omission was not caught in our short development time. I worked on the book a while after it was published, fixing some errata that I found. During this time, I finally developed a way to apply the drop cap automatically to the entries. Here is the solution, simplified a bit.

% Required Packages

% Setup lettrine
\input EileenBl.fd

% The Magic: finds first letter and first word in the proceeding text
% and passes them to lettrine

% Setup environment `entry' to use `entry*' with a drop cap
% Setup environment `entry*' so that lettrine can be manually specified if needed

This solution will not always work if the entry begins with something other than text; markup and figures can confuse it. However, for the few instances when I need to specify \lettrine manually, I can fall back to the entry* environment.

Sumatra PDF and LaTeX

I recently discovered a wonderful pdf reader for windows that makes working with pdfLaTeX a breeze: Sumatra PDF. (Yes, it has a whole Watchmen theme going on.) It is lightweight and easy to use. Unlike Acrobat Reader, Sumatra PDF does not lock the file, which allows you to overwrite it without having to close your viewer. Additionally, Sumatra will detect that the pdf has changed and reload the document staying on the same page.

I doubt Sumatra PDF supports all the latest features of Acrobat Reader, so if you have to work with a complex document, you can always fall back to Acrobat. However, for the majority of LaTeX documents it is the perfect solution. Combine Sumatra with TeXnicCenter, and you have a powerful, free solution for writing LaTeX-based documents on Windows.

Sexperts Under Fire


Abstinence-only education is a failure. Study after study has found that teenagers who receive abstinence-only education are no less likely to have sex as other teenagers, but are less likely to use protection when they do.

Now it appears that the prudes who brought us abstinence-only education in middle and high schools are targeting universities. According to the Atlanta Journal and Constitution, several Georgia politicians and religious right activists have become upset that the University System of Georgia has faculty members who are experts in human sexual behavior and diseases. These culture warriors are now making a bunch of noise to get the faculty members fired citing budget issues. As expected, these politicians are ignorant of academia, public policy, public health, history, and the law.

[Rep. Calvin Hill (R-Canton)] singled out Georgia State University, which lists in its 2009 media experts guide faculty members who are knowledgeable about male prostitution and oral sex. The guide is used by reporters and public policy organizations to find experts in various fields. Hill said he was “personally outraged” that tax money supports such professors.

His concern was echoed on the floor of the House on Friday by Rep. Charlice Byrd (R-Woodstock).

“Yes, ladies and gentlemen, you have heard me right,” she said. “In this present economy, the taxpayers’ dollars are being used by the Board of Regents to inform students about such social topics. … I believe the timing is perfect to eliminate positions of professors and staff who are paid to provide such services.”

Georgia currently lacks enough public health and medical professors to keep up with its growing population (which is why the Medical College of Georgia is expanding to Athens), and these idiots think that firing what experts the state has is going to improve things. Morons.

And it gets better; Rep. Byrd was so outraged that she used YouTube to let her constituents know:

Now a lesson in Georgia history.

In 1941, Gov. Eugene Talmadge fired several pro-integration faculty members.—Yes, the religious right is acting like a bunch of segregationists.—As a result of this political interference Georgia’s public universities lost their accreditation. In 1942, Talmadge lost reelection to Ellis Arnall, who had vowed to restore the integrity of the universities. While in office, Arnall led the passing of a constitutional amendment that completely severed control of Georgia’s universities from the politicians in Atlanta.


Paragraph I. University System of Georgia; board of regents. (a) There shall be a Board of Regents of the University System of Georgia which shall consist of one member from each congressional district in the state and five additional members from the state at large, appointed by the Governor and confirmed by the Senate. The Governor shall not be a member of said board. The members in office on June 30, 1983, shall serve out the remainder of their respective terms. As each term of office expires, the Governor shall appoint a successor as herein provided. All such terms of members shall be for seven years. Members shall serve until their successors are appointed and qualified. In the event of a vacancy on the board by death, resignation, removal, or any reason other than the expiration of a member´s term, the Governor shall fill such vacancy; and the person so appointed shall serve until confirmed by the Senate and, upon confirmation, shall serve for the unexpired term of office.

(b) The board of regents shall have the exclusive authority to create new public colleges, junior colleges, and universities in the State of Georgia, subject to approval by majority vote in the House of Representatives and the Senate. Such vote shall not be required to change the status of a college, institution or university existing on the effective date of this Constitution. The government, control, and management of the University System of Georgia and all of the institutions in said system shall be vested in the Board of Regents of the University System of Georgia.

(c) All appropriations made for the use of any or all institutions in the university system shall be paid to the board of regents in a lump sum, with the power and authority in said board to allocate and distribute the same among the institutions under its control in such way and manner and in such amounts as will further an efficient and economical administration of the university system.

(d) The board of regents may hold, purchase, lease, sell, convey, or otherwise dispose of public property, execute conveyances thereon, and utilize the proceeds arising therefrom; may exercise the power of eminent domain in the manner provided by law; and shall have such other powers and duties as provided by law.

(e) The board of regents may accept bequests, donations, grants, and transfers of land, buildings, and other property for the use of the University System of Georgia.

(f) The qualifications, compensation, and removal from office of the members of the board of regents shall be as provided by law.

Notice the two things I’ve emphasized. One, all the power to govern the University System of Georgia rests with the Board of Regents. And two, the legislature has no power over the budget of the USG. Simply put, the legislators are powerless to enact their fantasy. You’d think that they would have discovered that in all their budget “research”.

By calling for the removal of faculty members, Hill and Byrd have demonstrated their ignorance of academia, public policy, public health, history, and the law. Morons through and through.


It appears that other legislators, who have some familiarity with higher education, organized a smack down.

Two of those experts spoke to the House committee Tuesday. Kirk Elifson is listed as an expert in male prostitution. He said he became an expert while serving as a captain in the Army in Vietnam and later became a professor. The Centers for Disease Control, he said, sought out his expertise to help with the growing AIDS epidemic in the 1980s.

“We’ve done some cutting-edge research in HIV,” he said. “I’m proud of the work I’ve done.”

Oh, snap, they were dissing a veteran.

Mindy Stombler, another Sociology instructor, is listed as an expert in oral sex. She said her research is aimed at studying attitudes of teens toward sex, who, she said, are increasingly having oral sex and see it as “casual and socially acceptable.”

Several members of the committee praised Elifson and Stombler for their work, Hill, too, spoke to the committee but given the chance, did not ask the GSU faculty any questions.

Hill is still continues to be and idiot:

He argued that in a time of budget cuts universities should not offer classes that do not help students get jobs.

The University of Georgia is not a trade school. That’s Georgia Tech.

Science Gets the Shaft

US Senators Ben Nelson (D-NE) and Susan Collins (R-ME) are proposing to cut the stimulus/spending package by roughly 10%. Their staff have identified several “useless” programs included in the bill, and it appears that they consider science funding to be one of those useless pursuits.

Over the last 50 years, much of our economic development has been driven by science, and at a time when the US is faced with losing its scientific dominance to China and the EU, the US needs increased science funding. Give a man a fish, he eats for a day. Teach him how to fish, and he will eat for a lifetime. Fund fishing research, and your children all eat for a lifetime.

From the list of stimulus projects that are on the cutting block:

  • NSF 100% cut ($1,402,000,000)
  • NASA exploration 50% cut ($750,000,000)
  • NOAA 34.94% cut ($427,000,000)
  • NIST 37.91% cut ($218,000,000)
  • DOE energy efficiency & renewable energy 38% cut ($1,000,000,000)
  • DOE office of science 100% cut ($100,000,000)

If you have an opinion about these cuts, you should make it known to your Senators because they will soon be voting on this proposal.

List of Senators and Contact Information

Death Note


Looking for something to do? I recommend heading over to Hulu and checking out Death Note, an amazing anime series involving power over life and death. It is an amazing cat and mouse game between a police dective, L, and Kira, a vigilantle who executes criminals by writing their names in his God-of-Death notebook.

It may seem like a simple premise, but the plot is very intricate as both L and Kira develop plans to defeat the other by predicting each others moves. In nearly every case, they know exactly what the other will do, meaning that their plans must be elaborate. Its like cops-and-robbers played on a chess board crafted by the Grim Reaper. Their creativity and cunning are astounding, and just when you think one of them has won, the other one is ready with his next move. Simply amazing.

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This page is an archive of entries from February 2009 listed from newest to oldest.

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