In celebration of the successful defense of my dissertation yesterday, here’s the BioRad GTCA video.
Feel free to sing along.

A Bastion of Sanity in the Land of Oz
In celebration of the successful defense of my dissertation yesterday, here’s the BioRad GTCA video.
Feel free to sing along.
I finished The Pluto Files this weekend, the latest book by Neil deGrasse Tyson. Astrophysicist and Director of the
Hayden Planetarium at the American Museum of Natural History, Tyson is also a fervent advocate for science and making science understandable to the public.
The Pluto Files tells the story of Pluto’s reclassification, from ninth planet to dwarf planet. There’s the history of the discovery, along with difficulties involved in planetary discovery in general:
In an embarrassing example from January 1769, the French astronomer Pierre Charles Lemonnier did not discover Uranus six times.
That particular planet had been repeatedly classified as either a comet or a star. It was not officially recognized as a planet until 1781. As for Pluto, astronomers were searching for a “Planet X” to explain the perturbations in the orbits of Uranus and Neptune (perturbations which later turned out to be the result of poor estimation of the masses of the other planets, and not an undiscovered outer planet).
Tyson’s book describes the remodeling of the planetarium and the decision to classify the solar system by groups of related objects, and what that meant for Pluto in the grand scheme of things. The second half deals with the public fallout of that decision, from school children wondering where Pluto was in the display of the relative sizes of planets (and hundreds of crayon-illustrated letters to that effect), to other scientists who accused the planetarium administration of going against scientific consensus in grouping Pluto with other objects in the Kuiper belt. That was until the International Astronomical Union (IAU) voted to clarify the definition of planet. Currently, a planet is defined as a celestial body that:
While Pluto has met the first two criteria, it has not met the third (hence the name Kuiper belt for the region of icy objects where Pluto resides). The funny thing is, we’ve been here before. Ceres was declared a planet in 1801, and the number of planets in the solar system climbed to 23 as more were discovered. We later learned that these objects were actually members of the asteroid belt, not planets at all. Ceres didn’t have the cultural status of Pluto, though, and that’s what I found most interesting about The Pluto Files.
It’s a first hand account of how advances in scientific understanding can have a profound and direct impact on culture (and state legislatures). Both New Mexico and California passed laws declaring Pluto a planet, though California’s bill is a bit tongue-in-cheek:
WHEREAS, Downgrading Pluto’s status will cause psychological harm to some Californians who question their place in the universe and worry about the instability of universal constants; and…
WHEREAS, The downgrading of Pluto reduces the number of planets available for legistive leaders to hide redistricting legislation and other inconvenient political reform measures….
What should have been celebrated as an advance in human understanding of the universe was instead decried as desecration of a universal constant (that didn’t actually exist). And that is what makes people so uncomfortable. Science can change to meet the presentation of new facts, and that’s a good thing.
The following is an conversation that Dr. Tyson participated in at the LA Public Library following the release of The Pluto Files. He’s an entertaining speaker with a wonderful sense of humor, and it’s interesting to hear his perspective on the controversy.
I ran into an issue while doing some analysis for my dissertation. I’ve been working on comparing genetic distances between populations using a variety of molecular markers (mtDNA sequences, Y-STRs, and autosomal STRs). I wanted to generate several neighbor-joining trees to display the results, but I also wanted a way to test the statistical significance of the tree, or how accurate a representation of the underlying genetic distance data the tree actually was.
One way to do this is with bootstrapping, where thousands of random data sets are generated from the original data (by dropping data and recalculating the tree). In the end you have a tree with internal branch values, showing how many times each node turned up in the analysis. It’s a standard technique, and is the method I used with my autosomal STR data. But the software I used to handle sequence data in particular (MEGA, Phylip), starts with the raw sequences and generates bootstrapped trees from that data. The trees created show each sequence on its own branch, rather than each population. With over 8,000 sequences in my data set, this type of analysis really wasn’t useful.
But last week I found TreeFit, a little Windows program that generates an overall R2 value by comparing the genetic distance matrix with the distances calculated based on the neighbor-joining algorithm. Basically, it appears comparable to the STRESS value used for multidimensional scaling (MDS), measuring how well the representation of the data (the NJ tree) matches the variation present in the original distance matrix. A perfect fit would generate an R2 value of 1.0, while anything above 0.90 is considered a good fit (or an accurate representation of the underlying data). Values less than 0.90 suggest that another graphical display method (MDS) might be a better choice, as not all data fit the hierarchical model on which the NJ algorithm is based.
Using TreeFit, I got some reassurance that my NJ trees were accurate, and the statistical significance I needed to convince my committee that my data is not “merely descriptive.”
Technical specs:
The national AAPA meetings are in Chicago this week, which means that I and my fellow labmates have been busy the last couple of weeks getting our poster presentations ready (except for the one who shares my office and had her poster ready a month in advance, making the rest of us look like slackers). She had hers printed locally at the FedEx Office downtown, and with a 15% student discount paid ~$85.
I really didn’t want to pay that much to print my poster, or go through the hassle of dealing with printing issues at the local shop. The last time I had a poster printed I was at the copy center for hours while they tried to convince their printer to be nice and print the poster. Nerve wracking. While searching for poster templates online, I ran across PhD Posters. They have a few on-campus locations on the East Coast, but they can also FedEx your poster (overnight if need be, though that ups the shipping cost considerably). You just save your poster as a pdf and upload it to their site, make your payment through PayPal, and then wait for it to arrive. Best of all, printing rates for a 4′x4′ poster start at $39.99! With expedited 2 day shipping, I paid $10 less than my office mate. If I’d had the poster ready a week earlier, shipping would have been less than $7.
The poster arrived yesterday (a day ahead of schedule), and it looks fantastic. For those not yet living the postdoc high life, and paying conference costs out-of-pocket, PhDPosters is definitely the way to go.