Comp Bio is complicated

I finished up my first lab rotation two Fridays ago, here at UT Southwestern. It was a pleasant few months with an interesting project, consisting mostly of starting at a computer screen and writing Python scripts, running BLAST searches, and so on. To summarize, but leaving things vague (both for most-people-don’t-care reasons and the-data-is-unpublished reasons), the project was this:

There are currently a crap-ton (“crap-ton” is a standard scientific prefix) of bacterial and archaeal genomes published and available on NCBI‘s servers. Archaea, like bacteria, are single-celled prokaryotic organisms. However, they differ from bacteria genomically (and therefore metabolically) in many ways. Some archaeal properties are like those in eukaryotes (like us!), while others are like those in bacteria. So one of the huge unanswered questions in evolution is: how are bacteria, archaea, and eukaryotes related to each other? Or, how would we make a tree of life relating these three domains?

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A simple model of selection

Inspired by Dawkins’ METHINKS IT IS LIKE A WEASEL program (hereafter just weasel) described in his book “The Blind Watchmaker,” and wanting to practice my blossoming C++ skills, I decided to write my own version of weasel. It was successful enough, and I found the results interesting enough to warrant discussion. Download the program (Windows .exe file) so you can try it out for yourself (and you can also get the source code if you want). In this post I’ll discuss what the program does and why. In the next post I’ll talk a bit about the results of the program.


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Rabies is (are?) neat.

While going through all of my old school stuff from the UofC and uploading it into gmail, I came across the poster project I did for an immuno class at the end of my third (I think) year. It’s saved as a jpeg, so I put it up on flickr for anyone who’s interested in learning how rabies works. It’s pretty impressive how much it can do with so little genome. Anyway, click the image below to learn about rabies!

Dear Immune System,

Your time is up, and I am not pleased.

I first got this disease on Friday, five days ago today. It started with frequent trips to the bathroom and angry bowels. Then it got better the next morning of its own accord, and I thought that my brief excursion into sickness was done with.

So on Saturday I had a nice big meal. Too big, in fact, since I ended up with my belly so full that it hurt. But it still felt kinda good, after having been sick the day previously. But then the bathroom trips started again. And didn’t stop.

Sunday was spent entirely either in the bathroom or trying to sleep, in the vain hope that sleep would transport me into a disease-free future. I was rewarded in the evening with a fever.

Yes, body, I know that a fever is supposed to kill off whatever is attacking my insides (or whatever you have perceived to be attacking my insides), so why was it mild, and why was it gone the following morning, after accomplishing absolutely nothing? And it hasn’t come back, even last night when I was having even more frequent trips to el baño. What was the point?

And today I woke up and thought, “ah, it’s all over.” Since all I had was a slight belly ache. But as the morning went on it began to feel like someone had punched me oh-so-gently in the gut. Then I had a delicious meal and, before I could say “Not again!” it started again. The bathroom trips, I mean.

So to my innate immune system: I know you’re doing the best that you can with what you’ve got. You’re static, so really what more can I ask for?

But to my adaptive immune system: WTF? Now, I know you are one of the most amazing achievements of evolution, but seriously, can’t you just be a little more amazing? Perhaps you could work twice as fast, or fight twice as hard. I’d happily eat more to give you the spare parts and chemical energy. Or sacrifice some of my body fat for the task. Or muscle, even.

I know that’s too much to ask, since you’re fighting blind and quite randomly, which is why I have forsaken you and moved on to good old man-made drugs (all the cool kids are doing it). I’ve already lost a 6th of my trip to your taking of your sweet ass-time (yes, that is hyphenated correctly), and I am now cheating on you with generic, OTC, Mexican-made Cipro.

Now, adaptive immune system, this doesn’t mean I don’t love you and appreciate what you do, but when I’m on a deadline you just aren’t good enough. I’m sorry. I welcome you back as soon as the Cipro is done working (especially since I won’t have any gut flora left for defense).

Your Frustrated but Loving Counterparts,

The Higher Lobes

Or, the Ones That have to Perceive the suffering you’re supposed to be alleviating.

tRNA pun

I thought of this one day while brushing my teeth. The images make it easier, but this was the original joke:

So one tRNA diffuses up to another and says, “It is frigid in here!” The other tRNA responds, “Well, then go get your codon.”

Read it out loud to get the joke. It isn’t that funny, sadly, but it made me laugh when I thought of it.

The specific tRNA in the image is yeast Phenylalanine tRNA, which I got from RCSB. The number is 1ehz. I used pyMOL to orient and take the images, and then GIMP to add in speech bubbles.