Mad Prime

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).

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:

Was kind of sad this year having a "retreat" in a slightly different building in the same city. I amused myself by constructing a genetics "buzzword bingo" list.

1. Slide showing a signaling pathway with >= 15 proteins named
2. Messing with this gene causes cancer
3. Anything involving stem cells
4. Microarray data
5. High throughput / deep sequencing
6. RNAi
7. Animal model vaguely resembling a human disease
8. GWAS
9. Messing with this gene makes this tissue/organ look funny
10. Epigenetics
11. Mass spec data
12. FACS
13. Evolution
14. A photo that makes you lose your appetite
15. Apoptosis is mentioned
16. HAIRBALL (aka. "interaction network")
17. Anything related to sex (eg. chromosomes)
18. RNA splicing
19. Bacteria
20. Yeast
21. Plant
22. Worm
23. Fly
24. Fish
25. Mammal

Although silly, I found this actually helped keep me paying attention to talks. I applied it to the last session and almost got a BINGO, but Norbert Perrimon's signaling pathway slide only had 13 proteins. So close!

For some time now, I've been wanting to write about red-green color blindness, a dramatic perceptual difference with an interesting genetic and evolutionary story. This first post will mostly be an introduction to the topic. If you are color blind: I always feel guilty when I speak of this as a deficiency, or when I emphasize how profound the differences seem to the rest of us. I hope it doesn't bother you. I always wish I could pee standing up so... there.

Daylight vision in humans is mediated by the opsin proteins, which transmit signals that activate nerves when they are hit with light. Humans have three different opsins with different sensitivities to the colors of the spectrum -- it is the different color sensitivities that allow us to see color. You can call these the "blue", "green" and "red" opsins.

	A normalized diagram of the sensitivities of opsins to different wavelengths of light. "S" = "short wavelength", is the "blue" opsin. "M" = "medium wavelength", is the "green" opsin. "L" = "long wavelength", is the "red" opsin.

In its severe form, red-green color blindness occurs when a man is missing the "green" or "red" opsin - these conditions are respectively known as deuteranopia (1% of all males) and protanopia (another 1% of males). They are fairly similar in effect: a total loss of ability to distinguish hues in the green to red range. There are many less severe forms of color blindness -- 6% of males -- but that's a later post.

I say "males" because color blindness is almost always seen in men. This is because the "red" and "green" opsin genes are located on the X chromosome, which men have only one copy of. Women have two X chromosomes; even if one has inherited a deletion mutation, the other can serve as a back-up. For a woman to be color blind, both X's would have to carry the same mutation, which is much less likely to occur. (e.g. 1% * 1% = 0.01%)

I'll end this post by showing you what color blindness looks like. Vischeck is a service available online that simulates how images look to a color blind person. To a color blind individual the simulation and original images should look identical (or nearly so - computer monitors vary, so this cannot be perfect). If you're curious about the algorithm, the program is based on this paper.

Deuteranopia	Original	Protanopia

All colors in the red to green range -- green, yellow, orange, red -- are simulated here as yellow. As you can see, deuteranopia and protanopia are almost identical - the main difference is that red looks darker to the protanope (look closely at the picture of cars). Also interesting to note: the butterfly picture demonstrates how purple looks like blue to the color blind individual.

Credits: Opsin sensitivity diagram adapted from Wikipedia diagram, credit goes to User:Vanessaezekowitz and from the screenshot for Wavelength 1.3. Photos taken from flickr users Marshall Flickman, Teo, and Oneras under CC and CC-by-SA licenses.

Looks like my Genetics article was overdue for a "good article" rating. I think I'll work towards getting a featured article rating, the GA reviewer encouraged me to do this...

The double-blossom article was in the Did you know section of the front page for seven hours yesterday morning. It got the top spot, with the pretty double impatiens photo.

... that double-flowered mutants (pictured) were first documented over two thousand years ago by Theophrastus and are found in many popular flower varieties — including carnations, camellias, and most roses?

I made this new wikipedia article in the last couple days and have submitted it to the Did you know project for display on the main page.

Here are some previous posters I made for genetics department social hour, in reverse chronological order.