December 2008 Archives

Citation Station

I recently became aware of an October paper from Ian Holmes’s group at UC Berkeley describing a rich genome simulation toolset: “Tools for simulating evolution of aligned genomic regions with integrated parameter estimation” Besides their programs, what’s interesting about the paper is that they judged the quality of their work by comparing it to my own research. I have much respect for Holmes and to have him compete against a program from my dissertation research is an honor. Here is a choice quote from their paper:

We also compared our simulation methods, GSIMULATOR and SIMGENOME, to DAWG, a widely cited program for simulation of neutral substitution and indel events. We chose DAWG because it most closely exemplifies the goals we have identified here: it is clearly based on an underlying evolutionary model and provides tools for estimating the parameters of the indel model directly from sequence data. It appears to be the leading general-purpose simulator at the time of writing. Other simulators (such as PSPE) are richer, but do not provide the parameter-estimation functionality that DAWG does. (internal citations removed)

In other citation news, there is a new paper out in Genetics discussing the “hothead” mutation in Arabidopsis thaliana that made this blog semi-famous. This paper follows up on arguments that hothead’s revertant phenotype is due to unexpected outcrossing. They confirm that hothead does have a high outcrossing rate and that revertant phenotypes are due to outcrossed seeds.

When I first heard this argument, I kicked myself for not thinking about it first. What first characterized hothead plants was the lack of fusion in their flowers. Wild-type A. thaliana plants are complete selfers because their flowers are fused shut, preventing external pollen from reaching the stigma. This way, only pollen produced internally will pollinate A. thaliana. However, when the flower fails to close completely, external pollen is no longer excluded and outcrossing can occur. Duh!

Admittedly, this would have been hard to argue without having the actual plants because some observations reported in Lolle’s original paper conflict with outcrossing, but it appears that these observations cannot be replicated. Perhaps they were just artifacts.

Birthday Cake

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For my birthday last month, Tiffany made me a tasty cake, and I’ve finally “developed” the pictures.


I’ve already spent some of my birthday money on LittleBigPlanet.

The regular season is over and my system has determined the two teams that will play for the national championship: Florida and Oklahoma.

The Fighting PZs come in at #708.

4Southern Cal11-18.0956
5Texas Tech11-17.6739
6Penn State11-17.6547
9Ohio State10-27.1713
10Boise St12-07.0771

Some of you may remember that several years ago that Britten (2002) argued that human-chimp divergence was 5% not ~1.2%. (See this press release for a refresher.) Of course, creationists jumped on this research and began harping that the more scientists looked, the more distant humans and chimps were. This is important to them because the number one rule of creationism is “no matter what, humans are not related to any other living creatures,” which is so difficult to maintain in our age of science and education.—Amusingly, humans and chimps are so similar to one another that creationists cannot create a consistent definition of “created kinds” that makes humans special and lumps all the boring animals together.

Britten (2002) derived his 5% divergence metric by considering the lengths of insertions and deletions (indels) along with point substitutions between human and chimp genomes. This is unlike other estimates that just consider the number of point substitutions that have occurred between the two species and find ~1.2% divergence. At the time I commented that these two numbers—1.2% and 5%—could not be compared because they are different metrics. Additionally, Britten’s metric is probably unfairly upweighting the contribution of indels because a single event can add or remove multiple residues at a time.

A recent study of mine, which was not directed at Bitten’s work, has found that it is actually worse than that. Simply put, the total length of indels separating humans and chimps is unrelated to the evolutionary divergence between them. This arises because the variance of indel length is “nearly-infinite”, which causes nonconservation of average indel length. Therefore, two pairs of species, equally divergent evolutionarily, can and probably will have very different proportions of nucleotides belonging to indels. One pair might be 5% divergent and the other 1.5% divergent, including indels, without any underlying change in the evolutionary process or time since speciation.

The upside is that traditional substitution based evolutionary distances are unaffected and can still be used to properly estimate the evolutionary divergence between species.

Texas finishes just ahead of Oklahoma and should be playing in the Big 12 championship game according to my system. Florida’s hold of the #1 spot has narrowed. The first four teams—Florida, Texas, USC, and Oklahoma—have set themselves apart from the rest. The next four—Alabama, Texas Tech, Penn State, and Utah—are also set apart from the pack. If I was organizing a four or eight team playoff I have clear evidence for who gets in and who gets left out.

So what does this system say about the mess in the Big 12 South? Well when I parse it out into head-to-head, common opponents, non-common conference opponents, and non-conference opponents we get the following rankings:

  • Head-To-Head: Oklahoma, Texas, Texas-Tech
  • Common: Texas, Texas-Tech, Oklahoma
  • Conference: Texas, Oklahoma, Texas-Tech
  • Non-Conference: Texas, Oklahoma, Texas-Tech

Texas wins three out of the four categories. Although Oklahoma beat TCU and Cincinnati, they get really punished by the system for playing Chattanooga. I think Texas ends up favored by my system for several reasons:

  1. Texas beat Missouri, the best team in the Big 12 North.
  2. Texas blew out Kansas, the second best team in the Big 12 North.
  3. Texas’s cupcakes were obviously superior to Oklahoma’s cupcakes.
  4. Texas beat Oklahoma.

Not like that is going to satisfy anyone. … Today, we go up to 11 on the front page:

3Southern Cal10-18.1158
6Texas Tech11-17.6156
7Penn State11-17.6133
9Ohio State10-27.1159
10Boise St12-07.0287

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This page is an archive of entries from December 2008 listed from newest to oldest.

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