Archive for December, 2007

Compressing Time

December 27, 2007

 In 2007, I used my digital camera (a Canon PowerShot) to create a large pile of new media. According to iPhoto, I recorded 1,537 photographs, which averages to about 4+ new images every day. In order to objectively visualize my 2007 photographic habits, I created a video which compresses all my 2007 media into just three minutes and five seconds.

In the high-resolution (original) version, each photograph is shown for three frames at thirty frames per second. That’s 1/10 of a second per image. If each photograph was taken with a 1/100 average shutter speed, then this video is about ten times slower than reality. Despite this “slow” speed, the video is almost impossible to visually digest.

Happy Holidays Everyone: A LaTeX-thesis pack for the University of Oregon

December 12, 2007

A screenshot from Gmail, in which the Graduate School editor approves my thesis.
(view screenshot here)

If you’re writing a thesis or dissertation for the University of Oregon Graduate School (UOGS), here is a set of LaTeX files which will help you produce a document with approved formatting.

Download Here: (6.5 MB)

These files will help you format most of your document, but some hand-crafting might be required if your thesis or dissertation contains non-standard “stuff.” The instructions are in the file README.txt

Thanks to Peter Boothe for being a LaTeX-ninja, sometimes.

Five art-related blogs. . .

December 6, 2007

. . . which I recently learned about, are listed below. Peter says everyone-in-the-know has been reading (and loving) these blogs for years, which proves that I live in a solipsistic bubble of science, spiritual transcendentalism, and Stevie Wonder cover songs.

Here are the blogs:

  1. Boing Boing : a “directory of wonderful things”
  2. “We Make Money, Not Art”: art, design, media, and a nomadic computer scientist.
  3. Warren Ellis
  4. Beyond the Beyond: by Bruce Sterling.  This blog also includes a healthy dose of scientific futurism.
  5. The Wooster Collective: a celebration of street art.  To my credit, I’ve been reading the WC for a while, but only recently added it to Google Reader.

Summary: Metagenomics, fruit flies, and lessons learned

December 6, 2007

On November 8th, Nature published two cool articles about metagenomic studies of twelve Drosophila (“fruit flies”) species. In the the first paper (click here), The Drosophila 12 Genomes Consortium (D12GG) compared the complete genomic sequences of the twelve Drosophila species, which included the model organism species Drosophila Melanogaster. Although the twelve species are related, they exhibit a surprising amount genetic biodiversity. For example, the evolutionary distance between D. Grimshawi and D. Melanogaster is the same distance as between humans and lizards. As a side note, six months earlier (in May 2007), PLoS Genetics published a similar metagenomic comparison of Drosophila (click here for the paper). In the PLoS paper, Hahn et al. present the (somewhat obvious) conclusion: “the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss.”

On November 8, Nature also published this paper (click here), in which Stark et al. (including Hahn) used the data from D12GG’s research to demonstrate a truly novel insight about the connection between conserved metagenomic sequence motifs and functional elements. The result of this paper allows us to infer the presence of functional elements with a accuracy far surpassing previous methods. Specifically, Stark et al. show how to infer the following functional elements, based on a metagenomic sample:

  • Protein-coding regions: have highly constrained condon substitution regions, and indels have a bias for multiples of three.
  • RNA genes: tolerate substitutions that preserve base pairing.
  • miRNA: can be detected by looking for conserved palindromic stem sequences, which mutable loop sub-sequences between the two palindrome pieces.
  • Regulatory motifs: have high levels of genome-wide conservation.
  • Post-transcriptional motifs: are typically strand-based conservations.


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