January 2009 Archives

We Hath Frozen Over


It’s Obama’s first day in office, and he has already cured global warming.




Well the season is now over, and I can post the final, true rankings of all 726 the teams that play college football, based solely and objectively on their results and strength of schedule. As a result, Florida wins the 2008 Calix Cari.

2Southern Cal12-18.3860
7Penn State11-27.4032
8Texas Tech11-27.3976
12Ohio State10-36.9350
13Oregon St9-46.9265
14Boise St12-16.8864
16Virginia Tech10-46.7947
19Florida St9-46.7062
20Oklahoma St9-46.5858
24Georgia Tech9-46.4562

If you are concerned about how the truth of my rankings compare to the opinions of coaches and sportswritters, I’ve posted the Calix Cari rankings along side the Coaches’ and media polls.

Rank Calix Cari Coaches' AP
1 Florida Florida Florida
2 Southern Cal USC Utah
3 Texas Texas USC
4 Oklahoma Utah Texas
5 Utah Oklahoma Oklahoma
6 Alabama Alabama Alabama
7 Penn State TCU TCU
8 Texas Tech Penn State Penn State
9 TCU Oregon Ohio State
10 Georgia Georgia Oregon
11 Oregon Ohio State Boise State
12 Ohio State Texas Tech Texas Tech
13 Oregon St Boise State Georgia
14 Boise St Virginia Tech Mississippi
15 California Mississippi Virginia Tech
16 Virginia Tech Missouri Oklahoma State
17 Mississippi Cincinnati Cincinnati
18 Missouri Oklahoma State Oregon State
19 Florida St Oregon State Missouri
20 Oklahoma St Iowa Iowa
21 Nebraska Brigham Young Florida State
22 Iowa Georgia Tech Georgia Tech
23 Pittsburgh Florida State West Virginia
24 Georgia Tech Michigan State Michigan State
25 Cincinnati California Brigham Young

Compiling R Modules on FreeBSD

Installing modules for R can be tricky on FreeBSD due to differences between the compiler environment on FreeBSD and Linux. If the R module links against a third-party library, it is likely that the library will not be found without a bit off additional tweaking of the install command. On my FreeBSD 7.1 workstation, I have to use the following commands to install the GSL and Cairo R libraries, both of which link against external libraries. (They are wrappers to these libraries.)

install.packages(c("gsl", "Cairo"), configure.args=c("CPPFLAGS=-I/usr/local/include", "LIBS=-L/usr/local/lib"))

It would be nice if this was supported out of the box in R, but if you know the solution it’s rather trivial to do.

My latest paper has now been published by MBE. You can grab your free reprint by following this link. I earlier blogged about some of the implications of this research, which you can see here.


Insertions and deletions (indels) are fundamental but understudied components of molecular evolution. Here we present an expectation-maximization algorithm built on a pair hidden Markov model that is able to properly handle indels in neutrally evolving DNA sequences. From a data set of orthologous introns, we estimate relative rates and length distributions of indels among primates and rodents. This technique has the advantage of potentially handling large genomic data sets. We find that a zeta power-law model of indel lengths provides a much better fit than the traditional geometric model and that indel processes are conserved between our taxa. The estimated relative rates are about 12-16 indels per 100 substitutions, and the estimated power-law magnitudes are about 1.6-1.7. More significantly, we find that using the traditional geometric/affine model of indel lengths introduces artifacts into evolutionary analysis, casting doubt on studies of the evolution and diversity of indel formation using traditional models and invalidating measures of species divergence that include indel lengths.

Reference: Cartwright RA (2009) Problems and solutions for estimating indel rates and length distributions. Molecular Biology and Evolution. 26(7):473–480

This is funny on so many levels. A hardware store manager got so fed up with customers requesting male-male adapters for joining Christmas lights together that he posted a sign letting people know why he did not carry them. Male-male adapters are obviously dangerous, and it amazes me that people were asking for them.

I guess I can’t be that amazed; people tend to be lazy and stupid, and using a male-male adapter instead of following the proper procedures for joining strings of lights on a tree (see Deuteronomy) sounds exactly like something they’d think was a good idea. Didn’t they learn anything when California recently passed Proposition 8, which requires that all male-male adapters separate into two, lonely single male adapters? Female-female adapters are still considered a form of art (mostly interpretative dance).


And if you don’t understand this comment, I will not explain it to your sensitive ears.

I didn’t realize that using the wrong adapter is “possible immoral.” If the sign creator thinks those adapters are sinful, I’d hate to hear what he or she thinks of a Jenna Jameson movie.

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

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