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 To summarize, but leaving things vague (both for most-people-don’t-care reasons and the-data-is-unpublished reasons), the project was this: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?

Continue reading

More Puzzling

In a previous post, I discussed my attempt to write a program to solve a puzzle. I never updated that post because, well, I ran the program all night and it didn’t find the solution!

I had made up a fake puzzle that I knew had a solution for testing, and the program could solve it in 15 minutes. But it couldn’t solve the one I had recorded for the real puzzle. I figured (and hoped) that I had simply recorded it wrong and to check, I re-recorded the pieces and tried again. And it worked! Here’s how:

Continue reading

Homeopathy: Belly Flop to a Cure!

Homeopathy says essentially this: Something that causes disease can be made to cure that same ailment if the something is diluted into water so much that it is no longer present. For example, if you were to take one molecule of cyanide and dilute it into a swimming pool, then drink some pool water, you would be cured of cyanide poisoning! Sound too simple to be true? Well, that’s because you must first release the Energy of the cyanide. Personally, I do this via belly-flopping into the swimming pool, though any kind of concussion of the water will do. Punching the water is also a pretty good way to do it.

Another example: it is clear that humans are basically a disease of the earth. We’re polluting the crap out of it, killing all the wildlife, etc. Now, this should be easy to fix with homeopathy. Since people are causing these bad things on Earth, all we need to do is have someone go swim in the ocean, concuss the ocean, and then distribute ocean water all over the world. In the same way that you can dilute a cyanide molecule into a pool, you can dilute one person into the ocean. You still need to release the Energy of that person, though. I would suggest the concussion be from underground faults leading to earthquakes and tsunamis, though enough belly flops would likely also do the trick. I feel quite certain that there have been a few people in the various oceans when these kinds of concussive events have occurred, therefore it is clear that Sea Water can already fix global warming!

And while we’re thinking about it, just imagine how many things have been diluted into the oceans: people, animals, plants, drugs, chemicals, pesticides, fish nets, volcanoes, tsunamis, airplanes, boats, etc, etc, ETC! This means that sea water can stop volcanoes from erupting, release fish from nets, repair damaged boats and aircraft, fix broken bones caused by tsunamis and downed aircraft, release the hallucinogenic hold of LSD, cure various cancers, and so on. In fact, if you have a disease, all you have to do is jump into the ocean, and then you will be diluted to homeopathic levels, meaning your disease will be diluted to homeopathic levels.

Belly flop into the ocean. Then drink up. Any disease you have will be cured!


My mother gave the fam a new game for Xmas called “The Impossible Puzzle.” Or maybe that was the company name. Either way, the label is certainly apt.

The puzzle is composed of nine, 4-sided pieces with interlocking parts in the shapes of the 4 card suits (hearts, diamonds, etc). There is only one way to lock the 9 pieces into a 3X3 square, and the game touts the fact that “there are over 300,000 combinations, only one of which is correct.”

Fig.1: An example of the puzzle pieces.

My mother, her bf, and myself all fiddled with this puzzle for a while before becoming too frustrated. There seemed to be no way to logically sort through the options of all possible arrangements and rotations of the pieces and clearly a brute-force method of trying all combinations would take way too long by hand. But maybe not for a computer. So, I figured this would be an excellent opportunity to try out my programming skills.

Continue reading


This post discusses a computer program that you can download to try yourself (and get the source code if you want to make your own version).

At a family reunion earlier this summer, we were handed a wordfind that someone had generated somewhere on the Internets that contained the names of the family founders. I was solving mine and noticed that, as anyone has frequently observed, in any given wordfind you will find words that are not in the list. Presumably, this is due to the randomly-assorted letters, by chance, spelling out an unplanned word. Of course, the wordfind makers might also stick those in on purpose (for example, the family wordfind contained the website name multiple times) or purposely prevent some random words (profanity). Regardless, I began to wonder how often a word might appear in a word find just by chance. So I used the margins to scratch out a formula for the chance of finding a word of a certain length within a matrix of random letters.

Continue reading

Road thoughts

I drove to St. Louis yesterday to visit my Little Brother at WashU and to meet with a researcher tomorrow for a potential job. It’s a long drive, and my mind was whirring all the way, so I thought I’d throw out a few random things I was contemplating (my apologies for the unpolished, poorly-written quality):

I became (relatively) enraged when my new GPS lost signal near Iowa City. It uses satellites. In space. What could possibly cause the stupid thing to not have signal? Then I had no emotional response to getting pulled over for speeding. I wasn’t speeding that much, but it was in a construction zone. Turns out an investment in cruise control could have been worth it.

As I was watching the odometer, I realized that the tenths place is probably a floor function, meaning that it shows you the value .1 for .1 through .19, so that you would never know how many tenths of a mile you had actually traveled. Then I also thought that it could be a rounding function, so it would show .1 for .05 through 1.4, and I wondered which would be better. I think either could be better, depending on the situation, but no matter what you have a possible error of .09 miles. With the floor function, that error is all on one side of the measured distance. With rounding, you split it to both directions.

How would you find out which function was being used? The easiest way would be to get up to a constant speed (definitely should have gotten cruise control) and reset the odometer. Time how long it takes to get from .0-.1, and then from .1-.2. If these times are the same, it’s a floor function. If they are different, it’s a rounding function.

As I drove across some massive bridge in St. Louis, I marveled at human ingenuity. I was listening to Fox News Radio at the time, so I was simultaneously marveling at human stupidity.

I’m sure there were other disjointed thoughts, but it has now been a full day since then and I can’t recall anything else. My life is basically a dream, so if I don’t record anything it will all disappear forever. I find myself to not be terribly concerned about this.

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.


Continue reading