moving the lamppost

random musings of a molecular biologist turned code jockey in the era of big data and open science.

About

I have recently joined the trend of taking my blog ‘static’ rather than using a more complicated database driven solution like Wordpress. One major reason for me is that I like to write content in abstraction. I love LaTeX for this reason and I love Sphinx for the same reason. I chose Tinkerer as my static engine because it is actually built from Sphinx and it is written in my favorite language (Python). Sphinx is a code documentation framework originally built for python. I use it to generate my documentation using reStructuredText markup. I figured since I am more-or-less used to the way Sphinx does its markup, I would choose a blog engine that worked the same way. So far, I like it. It is a bit less mature than some of the other static engines out there (Octopress being a VERY popular one) but I think it will grow nicely.

The name “Moving The Lamppost”

Moving The Lamppost is a reference to the streetlight effect. I first heard the parable from a professor in my Probabilistic Modeling of Biological Data course. It goes something like this:

A police officer encounters a drunk fumbling around under a streetlight late at night and asks him what he is doing. The drunk responds that he is looking for his keys. The officer asks where he lost them. The drunk says he lost them across the street in the Park. Exasperated, the officer asks him why on earth he is looking for them over here. “Because this is where the light is,” responds the drunk.

In one sense this is something of a metaphor for some situations that we find ourselves in as scientists. We have a question we want to explore. An important one. But there are times when the tools available to us, or some critical idea or model related to our problem has yet to be created/formulated. So we go to work with the tools we have. This can cause much wasted time and money, however. So we must always have a couple questions in the back of our mind as we pursue our questions:

  1. “Am I looking where the answer is actually likely to be or simply where the light is?”
  2. “If I am stuck under a lamppost, is there a way to extend the reach of the light so that it includes the answer?” (Can I move this lamppost)

From another angle Moving The Lamppost can represent the most basic goal of science: to extend the edges of what is known.

The purpose of this blog

My main goal for Moving The Lamppost is to serve as a place for me to record random thoughts about my work and what is going on in science at large in such a way that I can engage in dialog with others about it. Relating to that goal is my desire to foster relationships with other scientists or informed hobbyists that can approach what is termed Open Science. I hope to make this my home base for sharing what I am interested in as well as what I am actually working on: including data and figures.

For a nice introduction to the ideals of Open Science take a look at the excellent blog series by David Ketcheson over at Science in the Sands

About me:

Augustine Dunn

PhD Candidate: Bioinformatics, Molecular Biology, Transcriptomics

I use bioinformatics to study gene regulation and expression at the transcriptome level. I currently work in mosquitoes. Specifically, I use RNA-seq and microarray technology to study how bloodfeeding affects gene expression in mosquitoes, and look for over represented patterns in regulatory DNA.

I use python, R, shell scripting and manage a local Galaxy instance to manage the lab’s bioinformatics and next-generation sequencing analysis needs.

The long term goal of my current lab is to produce genetically modified mosquitoes that do not transmit Malaria or Dengue Fever that will spread this trait swiftly through local mosquito populations.