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Archives for May, 2007

Troubleshooting with the Hive Mind

Late last week, my PCRs stopped working. One day I was able to amplify DNA from multiple different templates using different primers, and the next day I couldn’t. This is a major setback for me — a huge chunk of the remaining work I need to complete for my PhD involves doing PCR. If I…

Usually Choose Same

In yesterday’s post, I argued that, when flipping two unfair discs (or coins), there is a greater chance that both discs will land with the same side up than different sides up. As pointed out in the comments, I was assuming that the probability of heads is equal for both discs: Aren’t you assuming that…

Always Choose “Same”

The beginning of many Ultimate (nee, Frisbee) games is marked by flipping discs to decide which team must pull (kick off) and which goal each team will defend at the start of the game. This is sort of like the coin flip before an American Football game. Two players — one from each team —…

On Being Rated

Amongst the other TAs and the lab coordinators in my department, I have a reputation of being a tough grader. At the end of the semester, when the course admins calculate grades, my students invariably get a few points added to their lab scores — this is done to bring lab scores more in line…

A couple of weeks ago I suggested that the National Human Genome Research Institute (NHGRI) would no longer be funding de novo genome sequencing projects via white papers. They appear to be shifting their focus to resequencing projects to study variation (ie, this) and take a closer look at well studied organisms (ie, ENCODE, which…

Selection on Mitochondrial Genomes

Given the amount of attention I devoted to the effect of selection on the relationship between mitochondrial DNA polymorphism and population size (see here, here, here, here, here, and here), it’s only appropriate that I link to this article by Meiklejohn, Montooth, and Rand on selection on mtDNA. Here’s the abstract: Several recent studies have…

Attack of the Hybrids

For some reason, I have been collecting links to articles involving hybridization. That, on its own, would call for a massive link dump, but a recent news item makes for a nice contrast. First, the hybrids: Where better to start than this review of hybrid speciation — a topic I’ve discussed previously. The take home…

A Question for the Colorblind

I’m working on a few graphs for a presentation. In a previous incarnation, I distinguished two partitions of my data using the colors red and green. This made sense intuitively (the red ones had something broken, and the green ones were a-ok), but I realized that people with red-green colorblindness would not be able to…

Math for Biologists

Keith Robison, at Omics! Omics!, asks and answers the question, “What math courses should a biologist take in college?” His answer: a good statistics course is a must (one where you learn about experimental design and Bayesian statistics), and a survey course that covers topics like graph theory and matrix math would provide a nice…

Redefining the Binomial

There’s an interesting post over at Statistical Modeling, Causal Inference, and Social Science on calculating probabilities. Traditionally, if you observe a certain number of events (y) in some number of trials (n), you would estimate the probability (p) of the event as y/n. To calculate the variance around this estimate, you would use this equation:…