Mad Prime

Via David Nusinow on Google+:

When can we expect the last damn microarray paper? (http://jermdemo.blogspot.com/2012/01/when-can-we-expect-last-damn-microarray.html)

2016 for the last microarray paper? Sounds a bit optimistic, but we can dream. Of course there will likely be niche uses for microarrays for a while yet (e.g. cheap linkage analysis in a pedigree, as in my last post...) -- the analysis here is just counting usage of the word in the title (presumably indicating the technology is a major focus of the paper).

Reposted from Google+

Holy cow this is awesome -- this shows how platelets are formed as a megakaryocyte cell breaks up! My brother Andrew saw this in class recently, he showed me just now as we happened to be chatting about blood cell lineages. I think this should have more than 3500 views, so feel free to pass around!

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.

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!

This last Saturday Chris and I participated in a code jam organized by a friend using processing, a programming language oriented towards enabling interactive visualization and graphics. I used processing to create all of the graphs in the recent Nature Biotechnology paper - I came to it because I was frustrated with an inability to create exactly the graph type I wanted. In the end each of my graphs is created by a small program, but I'm happy with putting in that effort to get something that looks great.

For the code jam I had been wanting to create a browsable tree of life akin to the fractal-like tree of life comic I made a while back. To this end I created a Newick format tree, working my way back from humans. I filled in only organisms and names that were familiar to me, reasoning that obscure organisms only serve to make a tree confusing, cluttered, and unapproachable. So far I'm only as far as unikonts, you can get a copy of it here if you like. (Please consider this as licensed under CC-by-SA if you'd like to use it.)

Chris found and applied some java code for interpreting a newick format file and creating a tree data structure, and I worked out a simple recursion for drawing the tree out to a given depth from a given node. Clicking on a node redraws the tree from that location; pressing any key zooms back out by one level. Here is a screenshot of the base:

One of the nice aspects of processing is that visualizations should be portable to java applets. Although we haven't done it yet, hopefully we'll be able to do that. If you have processing installed, you can download a copy of what we wrote. (You'll need to fix the file path in the source code to point at the tree.) Other improvements I'd like to do: to make zooming smooth rather than jumping (this can be disorienting when a large change occurs) and add the ability to search and choose an organism, then color the tree according to distance from that organism so you can click "warmer" colors to get closer to it.

The theme of the event was "clocks" and although I had intended to work on this anyway, it did fit into the theme fairly well: we called the program "Evolutionary Time". We were thrilled to be awarded the "wealth" prize by processing founders Ben Fry and Casey Reas: a gift certificate to the MIT Press Bookstore, which I intend to spend on a reference or two for processing, hopefully to further improve our program. ;-)

I made this picture today in the new version of Inkscape, making extensive use of the new thin/thicken tool.

While reading up on giraffes and acacias on the internet, I noticed that the acacia featured in the original Science article wasn't in Wikipedia at all - not even a stub! The acacia, Acacia drepanolobium (Whistling Thorn) has a ton of info about it lying around on the internet, so it definitely deserves a wikipedia entry.

I found a creative commons photo on Flickr and the photographer, Martin Sharman, graciously changed the licensing on the photo to allow for commercial usage so I could use it in the wikipedia article. So I made the article, and I think the subject is pretty cool - this tree has a neat symbiosis with several species of ants, check it out.

The first known example of parasite induced fruit mimicry: Scientists report (in the April issue of American Naturalist) the discovery of a parasitic worm that infects ants and turns their butts bright red -- so they resemble berries. The parasite also changes their behavior, causing them to wave their butt around in the air. A bird spies the "berry", eats it up and is infected. Bird poop is fed upon by the ants, completing the parasitic cycle.

Science magazine had an article exploring a paradoxical observation: acacia trees fenced off and protected from herbivores seem to be less healthy. It turns out the acacia trees are usually in a symbiotic relationship with a species of ant that protects them. When nobody's munching on the trees, they stop providing for the ants and the symbiotic relationship breaks down -- in a way that's actually worse, in the end, for the acacia.

Then I started wondering, tangentially, if giraffes and acacias coevolved tallness. So I googled around... what I actually found was some surprising controversy regarding the evolution of the giraffe's neck.

Everyone pretty much assumed they evolved tall necks to reach more leaves, but in 1996 a couple of guys proposed that the neck was actually a product of sexual selection. Turns out that the males use their necks as weapons when fighting each other. Check out this crazy youtube video. (url: http://www.youtube.com/watch?v=C7HCIGFdBt8 )

The argument they had against the feeding hypothesis was that giraffes spend a lot of time browsing at or below shoulder level. In 2007 another group published a study which found that higher quality biomass was available to giraffes higher up, due to competition with other foragers at lower levels. In the end I think I'll stick with the tall-to-reach-leaves-hypothesis, but I thought this video of fighting giraffes was too awesome not to share.