from the desk of stinkpot

Our paper on ancient genome evolution was published online yesterday.  It’s been remarkable watching news stories about the work spread online; as a scientist and geek, it’s thrilling to see my work on sites like Wired or Slashdot.  There’s also been some press coverage from less techie sources, like MSNBC and US News. To which […]

I’ve recently started my last (hopefully) thesis project on my way to my PhD. The project will be a study of the human gut microbiome; to analyze it, I’ll be embarking on an investigation of several months worth of human feces.  (And, if that high-level description grosses you out — be very afraid of the […]

i don’t think i’ve blogged about this topic yet; with the aid of some wonderful experimental collaborators and my advisor, i co-authored a paper in science this past summer on microbial ecology. my contribution to the project was an algorithm i named AdaptML. it’s a pretty cool algorithm*: i think it’s one of the first […]

i got a little distracted lately and began designing our lab website. i ended up getting a lot distracted; iweb is incredibly easy to use and making extremely visually appealing websites with very little effort is addictive. if you’re interested in getting to see what happens when abercrombie & fitch meets a microbiology lab, check […]

arthur c. clarke passed on today.  i just read his obituary and learned that he was the original author of the aphorism: “Any sufficiently advanced technology is indistinguishable from magic.” the next time i try and explain microbial evolution to someone, i think i’m going to quote mr. clarke.

meet hubert, my octopus.  he came to visit last week while i waited for some particularly long modeling jobs to execute on the darwin computing cluster (more on that later). hubert’s timing couldn’t have been better, as his visit coincided with ned ruby‘s to mit.    here’s a picture of ned: ned is a microbiologist from […]

i narrowly passed my thesis proposal defense the other friday. it wasn’t catastrophic or anything like that, but it certainly didn’t go as well as planned. for one thing, the oral examination was much more serious than i had anticipated. i hadn’t been so naive as to think my orals would be fun — a […]

while making slides for my thesis proposal this friday, i came across this beautiful triptych of a macrophage attacking an e.coli cell. this painting definitely needed to shared; it does a fabulous job of illustrating how remarkably dense a living cell is. (the fact that interacting biomolecules find one another amidst this mess is proof […]

this is nuts.  blackwell publishing wants $54.83 for a 3 page paper about a program that runs 2 statistical tests. if not for the institutional license, i bet you’d find half the scientific literature on bittorrent.

a fascinating read this morning on students who receive phds in the natural sciences from secular institutions – and continue to insist earth’s origins were biblical in nature. i find it remarkable that anyone can sufficiently digest geoscience literature to write a decent doctoral thesis – and still remain unconvinced enough to buy into a […]