Allele frequency problem in “Looper”

Time travel movies are always full of bad physics and and contradictory logic, though certainly some do it better than others. I usually just try not to think about them too hard so that I can take in the entertainment value. Looper (streaming|DVD) is no exception, but the most glaring error in the movie’s science was not in the physics; it was in the biology.

The beginning of the movie tells of a new mutation, the “TK mutation”, that has crept into the population to give people weak telekinetic powers. The idea of a gene, and more importantly a mutation in an existing gene, somehow allowing telekinesis is of course absurd, but that isn’t what I’m talking about.

I’m talking about the allele frequency. The movie takes place in the 2040’s. Only thirty years from now. And, at that time, the movie says that 10% of the human population has the TK mutation. This frequency is fantastically improbable.

Why? Well, right now 0% of the human population has this mutation. The thirty years between now and then have to bring that to 10%. That sounds impossible – let’s see if my suspicion is correct.

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 To summarize, but leaving things vague (both for most-people-don’t-care reasons and the-data-is-unpublished reasons), the project was this: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

weasel_title

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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.

Evolution Confusion [1]

Note: This was a detailed response to post about evolution. The post contained a lot of common misconceptions, so I wanted to take the opportunity to try dispelling them.

Evolution: A Modern Paradox

In today’s culture, evolution has permeated people’s worldview and has changed science into a new meaning.

As far as I understand, the definition of science has not changed as a result of the discovery of evolution. What is the older meaning that has been supplanted, and with what newer meaning?

Evolution is a matter of faith, certainly not scientific fact, because there is no solid proof supporting the theory. No one was there to see what really happened, and it contradicts proven scientific law.

Actually evolution is a matter of scientific fact. Your confusion comes from the extremely common misunderstanding of what science does. Science does not prove anything. Ever. The scientific method is a process where observations are made and models are proposed to explain these observations. These models are also known as hypotheses.

For any given set of observations there can be many different hypotheses that explain the data. Some hypotheses might seem more reasonable than others, but you cannot prove that any one of them are correct, though you can certainly prove some wrong. So the scientific method continues by collecting more data and trying to determine which hypotheses best fit the new data.

This is where experiments come in. Not all science is experimental, since experiments are things where conditions are manipulated by people. We simply can’t manipulate anything we want (like in evolution where we can’t go back in time, and astronomy/cosmology where we can’t manipulate giant, distant bodies). Experiments are useful because they allow us to throw out alternative hypotheses that don’t shed any light on the data.

For example, let’s say you wanted to decide if beer bread made with dark beer tastes better than that made with light beer. I hypothesize that dark is better, based on the fact that I think dark beer tastes better (taste of beer is the data). So, I need to collect beer bread taste data.

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