Mad Prime

I've decided an online ordering system I've been using is actually an interactive modern art piece, designed to provoke a response in the viewer to the experience of bureaucracy. Emotions of helplessness, confusion, and frustration are created through the thoughtful assembly of layers, pages, numbers, and forms. With this new appreciation I find my heartrate subside -- I chuckle at how I was manipulated by such clever design.

I don't know how I found time to do this. It didn't take that long. I was supposed to do a 4th-of-July patriotic theme but got distracted.

I defended last Thursday. People claim I gave a good talk. My sister (who is pretty nonscientific) claims she understood large segments of it!

Chris recorded the talk with audio and video. It was hard to read the slides on the original video, so he's created a video using the audio only and pics of the slides themselves.

I should watch it myself, but dislike the sound of my own voice... I think I sound like a chipmunk. Honestly, in my head my voice is much deeper than that.

Anyway, if you take the time to watch, I hope you enjoy it! The subjects are epigenetics, DNA methylation, and a little on clinical analysis of whole genomes (related to the Personal Genome Project).

Since Chris's blog post about his t-shirt seems to have been a hit, I should post about it here as well. The story is this ... Chris has been wanting to learn electronics for a while, so when SparkFun Electronics had a give-away in January he jumped at the opportunity and got $100 worth of electronics (this deal was given out to 1000 people). This stuff included a LilyPad Arduino and LEDs, etc. For a while Chris brainstormed on what to make with it and decided to make a T-shirt that reports how many emails are in his inbox.

I helped out too, I'm responsible for the design: vertical binary LED layout, the custom T-shirt printing (from cafepress), and all the placement and sewing of items onto the shirt.

More recently we attended PAX East this weekend. On Friday Chris wore another custom shirt we ordered from Cafepress (pictured on the right). The idea for the text was entirely Chris's (he came up with it over beer at a post-Libre Planet party at the Acetarium); Mako suggested the font choice (Impact). I think it's hilarious. If you don't get it, try watching this Daily Show Chatroulette skit.

My physic friends network confirms that this is not a hoax:

http://en.wikipedia.org/wiki/Color_confinement

Here is the lead pic and accompanying caption:

The color force favors confinement because at a certain range it is more energetically favorable to create a quark-antiquark pair than to continue to elongate the color flux tube. This is analoguous to the behavior of an elongated rubber-band.

Quick, reroute the color flux tubes to divert color force into the hadron jet! (The principle is simple, really, it's just a rubber band but made out of pair-bonding quarks.)

Biologists and other fields have been content to develop their secret lingos using a few new words and a lot of acronyms. It never occurred to us to simply re-use common words to mean utterly different things so that when I'm talking about "underpants" I actually meant "retrotransposons". That genius is reserved for physics.

ExploreTree, a processing program I've made for displaying and browsing tree data structures, has been rewritten and features have been added. New features include:

• Two modes of drawing: "slanted" and "radial" (see pics below)
• Two methods of avoiding overlapping node names: "nudge" and "hide"
• Dotted lines indicating more of the tree lies beyond an outer node
• Dynamic tree depth: adjusts depth so that there is never more than N nodes visible

Old features still there are:

• Search for organism & path highlighting
• Click to move to a node
• Forward and backwards movement with arrow keys
• Font adjustment & tree depth adjustment
• Right-clicking on a node (or control-click for Macs) opens up the corresponding Wikipedia page

The main version of the tree, a manually created tree I've made, is on the main site www.exploretree.org. Here is an image of it as a "slanted" tree with "nudged" nodes, near "rose" (to which the path is highlighted):

The original version of the program had no ability to display branching distances, but the new version does. You can see this when the it's used to display a tree downloaded from Interactive Tree of Life website. Here is an image of this as a "radial" tree with overlapping nodes "hidden", within Metazoa (aka. "animals") and the path highlighted to Homo sapiens (aka. "human"):

In addition to the new features, part of the motivation for this update was that I can envision a lot of adaptations of this program for specific uses. The original version's code was all entangled, making it extremely difficult to modify. This re-write has attempted to modularize the code a fair amount. At the very least this will make it easier for me to create spin-off programs from it in the future. Maybe a version that can read in "GEDCOM" genealogical data to make family trees -- the age of the parent at birth can be used to determine branch lengths!

People often note how the internet enables hypochondria, by allowing you to see a multitude of conditions -- some exceedingly rare -- that happen to match your symptoms. But if you don't abuse it I think it's actually quite helpful.

I did a lot of walking today and this evening I noticed my left foot had a sore spot. I described it to Chris (verbatim, this is cut-and-paste from chat): "around my toes, on the left foot like... the joint where the knuckles are on the hand, around my third and fourth toes".

I kept poking at it, wondering if it was bruised inside, trying to remember if I'd stumbled and banged it earlier in the day. So I tried the net....

It turns out this is an spot-on description of the localization of Morton's Neuroma -- weird scary name, but really a very common foot problem. My case is quite mild, I'll take it easy and let the irritated nerve & inflammation relax. It can be caused by bad arch support -- I've been told before that I should use arch-support inserts, so I should get a pair for these shoes.

Hah! It looks like there's a protocol for DNA hybridization in blots using 5% Irish cream liquor! I kid you not. Here's a sample quote from the methods of Yamamoto et al. 1993:

Hybridization was carried out overnight at 65°C in a solution containing 6 × SSC, 5% Irish cream liqueur (Original Irish Cream, R & A Bailey's), 20 mM Na₂HPO₄, 20 μg/ml heat-denatured salmon sperm DNA, and 2 μCi/ml of the ³²P-labelled probe.

The original source appears to be Elbrecht, A. 1987, "Lab Hints: Irish Cream Liqueur as a Blocking Agent for DNA Dot Blots." BM Biochemica, 4:12-13. BM = Boehringer Mannheim, it appears to be a newsletter. It's too obscure for my cursory searching to turn up a copy of the original, I wonder what the motivation was! Maybe this way you can order liquor using grant money? This idea has a lot of potential...!

The New York Times has a nice article on flower evolution today.

If you enjoy looking at evolutionary trees to see how closely related different living things are, you might enjoy playing with ExploreTree. I've added features that make it a lot more fun: the zooming in and out is animated, you can search for an organism and follow a path. Plus now, with a little help from Chris, it runs on a webpage (feel free to show it to friends & family). Give it time to load, though.

Here is a snapshot of the location illustrated in the NYTimes article:

I've put off posting about the program for a while since I kept hoping to improve it a little more, but here it is. It was written in processing, you can get the code if you'd like to play with it here (or improve it!) on github.

Another social hour poster illustration: