Friday, November 23, 2012

Coffee in Socorro, New Mexico

My mother's family is from Socorro, New Mexico, which is where I'm spending my Thanksgiving vacation.  Socorro is an interesting town; it's in the rural plains south of Albuquerque, a land of libertarian ethics and every man for himself.  But it's also the location of New Mexico Tech, formerly the New Mexico School of Mines, a school with strong geology, physics and math programs.  Many of the scientists at NM Tech came from Los Alamos, or work at the National Radio Astronomy Observatory or the Very Large Array (as seen in the movie Contact).  My grandfather was the registrar at School of Mines for his entire career.

It is interesting sitting in the coffee shop here.  It's a new addition to town; at the next table, there are four old men with gray beards and cowboy boots, eating scrambled eggs.  And conversation is moving smoothly between national politics, football, master's theses surrounding natural selection, local Rhodes scholars, cabinet positions in the state of New Mexico, and the stock market.  Yes, Socorro is a very interesting place.  Just thought I'd share my amusement at how easily our stereotypes can be broken down.

Tuesday, October 23, 2012

Cognitive overload

Just a quick note about this blog post by an old friend of mine from Wesleyan, David Jay.  This fits so nicely with my experience of going into a career in statistics and computer science from the launching pad of biology.  At first, the concepts are just too much and my brain wants to shut down.  For me, so much of grad school thus far is repeating exercises over and over until my brain can start to handle these concepts more automatically.  It's similar to learning the muscle memory for a kayak roll or when playing a piece on the piano; it's rote repetition at first.  Finesse and creativity come later.
  A note on the picture: I tried to find a photo of David on rollerblades, which were his predominant mode of transportation in college.  No luck; this picture will have to suffice.

Tuesday, September 25, 2012

Who uses morse code anymore?

So, funny story: today I was talking with my acquaintance Beth; she works at the Laboratory for Atmospheric and Space Physics at CU.  She asked me what my major is, and I told her I'm a computer scientist.  She then told me that at LASP, the computer scientists are basically the only ones that can communicate with any telescopes, satellites, or other orbiters that we send into space.  Apparently, one of their recent missions got up into space and the scientists on the ground were able to retrieve information from it, but there was a system failure that meant they couldn't send new commands or controls to the satellite.

Computer scientists to the rescue!  According to Beth, the information gurus translated their instructions into Morse Code to communicate with the satellite.  Probably not something they widely shared, but nonetheless, quite cool.  My reply to this story: to a computer scientist, information is information, no matter how you encode it.  Reminded me of the recently released DNA-encoded book by George Church at Harvard.  Here's Carl Zimmer's blog about it.

Anyway, it was good to hear that Morse Code is alive and well and rescuing our space missions!

Tuesday, September 11, 2012

Apply for the Omidyar Postdoc Fellowship

I'm posting this because I spent time at SFI in the summer of 2011, at their Complex Systems summer school.  If you're interested in cutting edge, self-directed interdisciplinary research, this postdoc is for you!  Also, Santa Fe is a great city.
SFI is recruiting Omidyar Postdoctoral Fellows!  

The Omidyar Postdoctoral Fellowship at the Santa Fe Institute offers:
• transdisciplinary collaboration with leading researchers worldwide
• up to three years in residence in Santa Fe, New Mexico
• discretionary research and collaboration funds
• a structured leadership training program
• unparalleled intellectual freedom
Deadline: 1 November 2012. 

The Omidyar Fellowship at the Santa Fe Institute is unique among postdoctoral appointments. The Institute has no formal programs or departments. Research is collaborative and spans the physical, natural, and social sciences. Most research is theoretical and/or computational in nature, although it may include an empirical component. SFI typically has 15 Omidyar Fellows and postdoctoral researchers, 12 resident faculty, 100 external faculty, and 250 visitors per year. Descriptions of the research themes and interests of the faculty and current Fellows can be found at

Requirements include a Ph.D. in any discipline (or expect to receive one by September 2013), an exemplary academic record, strong quantitative and computational skills, a proven ability to work  both independently and collaboratively, a demonstrated interest in multidisciplinary research and evidence of the ability to think outside traditional paradigms. The Santa Fe Institute is an equal opportunity employer, and women, veterans, and members of underrepresented groups are especially encouraged to apply.  U.S. citizenship is not a requirement.

The SANTA FE INSTITUTE is a private, independent, multidisciplinary research and education center. SFI seeks to catalyze new collaborative, multidisciplinary research; to break down the barriers between traditional disciplines; to spread its ideas and methodologies to other institutions; and to encourage the practical application of its results. The Omidyar Fellowship at the Santa Fe Institute is made possible by a gift from Pierre and Pam Omidyar.

For additional information or assistance, please email ofellowship at santafe dot edu or fax 505-982-0565

Tuesday, June 26, 2012

The Story Behind the Atlantic Salmon

What an interesting morning.  I started off by finding a post on a friend's Facebook page linking to this article by Jonah Lehrer in the New Yorker about the decline effect, from December 2010.  (For those of you who prefer to listen to your news, Radiolab did a short podcast called "Cosmic Habituation" summarizing the article here.)

Of course, I sent the New Yorker article along to my lab group, and my advisor (Aaron Clauset) responded with a link to an even better summary of p-values and the resulting bias in the scientific literature by Carnegie Mellon professor Cosma Shalizi, entitled "The Neutral Model of Inquiry (or, What is the Scientific Literature, Chopped Liver?)."

These collection of articles and posts summarize the related issues of false positives, stochastic effects resulting in positive results that may or may not be significant, and the file-drawer problem.

But really, I like my educational experiences to be thoroughly hilarious, as well.  So, ladies and gentlemen, I refer you to the second link in Prof. Shalizi's post, The Story Behind the Atlantic Salmon.  Because, really, if you can't derive significant scientific discoveries from dead ichthyological specimens purchased at a local grocery chain, how are any of us to make sense of this curious existence?  Enjoy.

Wednesday, June 20, 2012

Six Provocations for Big Data

danah boyd, author of the article
Today at the BioFrontiers Institute we had lunch with undergraduate students in the SMART program, who are doing STEM research for 10 weeks at the University of Colorado.  Our conversation over lunch about ethics, especially related to data sharing, reminded me of a great article about Big Data that I read last semester.  I'm going to post it here so that next time I'm interested in reading it, I don't have to dig quite so deeply into my gmail archive. :)  Without further ado: Six Provocations for Big Data.

Thursday, May 31, 2012

Stigler's Law

Stephen Stigler himself.
As a reminder to my fellow grad students out there: I know we are all in this academic endeavor for the pursuit of knowledge, correct?

Hahahaha, yeah right.  What we really want is to go down in the history books for our significant contributions to science.  Well, in that case, remember that you in fact should strive to be the second person to discover a law or property.  As Stigler's Law notes, "No scientific law is ever named after its original discoverer."

So, peers, get to reading those old obscure journals.  If you rediscover it, you've got a much better chance of achieving infamy in your miniscule niche of science.

Thanks to the Wiki article on Benford's Law for pointing me towards Stigler.

Thursday, April 19, 2012

A new era in Computer Science?

A few good articles have showed up recently in my two favorite publications about the future of Computer Science.

First, the New York Times ran an article a few weeks ago about the president of Harvey Mudd College (where my mother applied, got rejected, and was invited instead to be a part of the inaugural class at a new women's college in the Claremont system, Pitzer). Central to Dr. Maria Klawe's success at Harvey Mudd in increasing the proportion of female graduates in the Computer Science department was changing the standard curriculum to emphasize the cross-disciplinary applications of Computer Science. As the article put it, the introductory CS class was divided into two separate classes: a "hard-core programming" version in Java, and a version where "the focus of the course changed to computational approaches to solving problems across science."

Second, the Atlantic Monthly ran an article this week about how innovation in the tech start-up industry is stalling...we are recycling old ideas and, worse, exporting the best minds in CS to work toward increasing online advertising revenue.

It seems like these problems are interrelated. As the Atlantic article puts it, "[Developers] keep tossing out products that look pretty much like what you'd get if you took a homogenous group of young guys in any other endeavor: Cheap, fun, and about as worldchanging as creating a new variation on beer pong." Maybe if industry and academia can continue to reform both the stereotypes and the very definition of Computer Science, we can move beyond increasing revenue, to using our computational resources to improve our quality of life and our understanding of the world around us.

Tuesday, March 13, 2012

The Nine Circles of LaTeX Hell

My advisor sent out this link yesterday. I am hovering somewhere between level 8 and level 9 of LaTeX hell. Time to get on that...

Amusing, nonetheless.

Tuesday, February 7, 2012

Snow Crash

So I'm really getting into pleasure reading. After spending all day coding or doing biophysics problem sets, it's nice to escape into the world of ideas. And wow, Snow Crash is some serious escapism. First things first: when I finished it last night, I read the acknowledgments and one of the first people mentioned for his contributions was Dr. Steve Horst, a professor of philosophy at Wesleyan University. Go Wes! Second, you just can't describe this book. I tried to tell a friend about it the other day, and I ended up blabbering on about the dystopian privatized franchise-lands of the future, and how teenagers got around on super-skateboards, and how viruses were being spread in virtual reality, and there are nuclear weapons, and...listen, this just doesn't do it justice. Let me just say this: the main character's name is Hiro Protagonist, and he fights with samurai swords. Just read it and you'll understand. As for me, I'm glad it's done so I can finally get some sleep again instead of staying up reading until wee hours of the morning.

Monday, January 23, 2012

The Sheltering Desert

I just read this book for fun. I would say I have unique tastes in literature, but I loved this. Written by a German geologist in hiding during WW II, it combines descriptions of the Namib desert, the wildlife that inhabit it, and philosophy about the nature of humanity in a non-cheesy way. Pure escapism, and I could've kept reading for about 300 pages, easily. I was sad when it was over. I hope someday I can go visit the Namib and see the landscape and the shelters that Henno Martin and Hermann Korn built over their two and a half years in hiding in the desert.