Image correction in fluorescence microscopy

My paper on image correction comes out in Nature Methods in June (and is available online right now). Sorry for the paywall; this is an unfortunate consequence of working at a major research university. I’m not allowed to post pre-print versions of the paper until 6 months after publication, but I will definitely do so as soon as I can!

The story of the paper is below.

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Responsive Web design

Figure 1: While pixel density is all over the place, the actual physical dimension nicely separates each device (gray line at 7in).

As I evolve closer towards the status of full-fledged professional, I continue to realize that my web presence should reflect that development. For this reason, I decided that it would be wise to re-tool my website. I need to separate the professional and less-professional aspects (though I’m not sure any of my content really is “professional”), and stick everything under a resume-like landing page. I have enough posts here that this will be a major project, especially since some posts still receive a few hundred views per month. And because I have forgotten most of the web design skills I used to have (which were minimal in the first place).

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Monocles

My brothers have finished and launched their first totally independent game from our game company, Butterscotch Shenanigans. It’s called Towelfight 2: Monocle of Destiny. It is exactly as insane as the title suggests.

I had a lot of fun testing and watching as the game progressed and, even if I didn’t have an automatic bias, I honesty have to say that the game came out amazing. It is getting rave reviews everywhere, with the only consistent complaint being about the controls. But it’s a dual-stick shooter on a touchscreen, so the controls are destined to be at least a little annoying. The bros did push out a final patch on Android (and that will eventually make its way through Apple’s iTunes guardians) that fixes the control issues as much as possible.

Go download it on Google Play, Amazon, or iTunes and start shooting animals out of your face! It does cost a little cash ($3) but is definitely worth skipping a latte for!

CPR

The weekend of my last post (over a month ago…) my brothers and I did indeed complete a Game Jam with a crazy game called “I know CPR!”. It was a little inspired by QWOP (though it is not even almost as difficult) and otherwise followed the theme for the weekend: the sound of a beating heart. The executables (PC/Mac) are free to download, so go try it out (and see the video below)!

Game Jam this weekend!

My brothers have been toiling away over the next Butterscotch game for the past few months, and I have contributed nothing to it. In fact, my last contribution was to a game that we decided to scrap last October. First I got focused on NaNoWriMo, and then decided that I needed to start paying attention to that whole getting-a-PhD thing…

So the annual Game Jam is this weekend, and will be a perfect opportunity to take a break from research and pound out a game with a short deadline. And get back into touch with the family in an oh-so-productive manner.

And then I can get right back to SCIENCE!

average gene length in prokaryotes (part 2)

Hm. So it appears that, two years ago, I wrote a post on calculating the average gene length in prokaryotes. I found a half-draft of the second part and decided to finish it off.

In part 1 we defined mGenes (“maybe-genes”) as the pieces you get after breaking the genome at each stop codon, and predicted that the probability of finding an mGene of length L is given by the following equation:

Equation 1: The probability of finding an mGene of length L.

By plotting this function it is clear that the probability of a set of codons being an mGene plummets quickly, so that there is nearly a 0 probility of finding an mGene of 100 codons (300 bases) in a random sequence (black line in Fig. 1). I confirmed this with a 1,000,000 base synthetic genome (all code is at the end of this entry), resulting in the red circles in Fig. 1 that perfectly overlap with the prediction line.

Fig. 1: Predicted frequency of mGenes. Red circles, results from 1Megabase simulated genome. Black line, function shown in Equation 1.

So now we know what to expect from a completely random genome: Nearly all mGenes will be less than 100 codons (300 bases) in length. This is much shorter than your typical gene, and so I would expect there to be a large number of mGenes larger than this size in a real genome. So let’s check it out, using a fully sequenced prokaryotic genome!

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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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