more on rotations

It’s funny to me that I would have been perfectly happy not doing rotations at all, but since I am, you’d think I was choosing a partner for life. Four times! Nevertheless, here’s an update: I met with Ian Korf, and I’ve emailed Scott Dawson and David Begun. Next week, I’ll meet with Scott and David to talk about possible projects.

So, that leaves one more. Katie Pollard, I think. I haven’t talked to her yet. I’m not sure why not. I’m also thinking that I want to get a Master’s in Biostatistics while I’m at it. I can’t decide if that means I should definitely do a rotation with a statistician or if should do one with a microbiologist since I’ll be getting plenty of statistics. I’m thinking I should talk to Mitch Singer and/or David Mills and/or Kate Scow. Yeah, so I guess I haven’t really narrowed it down that much. Crap. I may be thinking too much about this.

droppin’ like names

I’m planning a trip this summer that I’ve dubbed the “Fly Hunt.” Really, I’m going to NESCent to take a 10-day course on Phyloinformatics. I figure if I have to go from the west coast to the east coast and back, that I should drive. I’m aware (only because I’m often told) that this is an unusual response to a need to travel 6000 miles, but I feel lucky to have the opportunity. I’m going to collect flies (Drosophila) along the way.

So, I’m looking for people along the way who will take me on a local collecting trip. I don’t really know one species of fly from another, and if not an orchard, winery, or fruit stand, I don’t know where to find them. So, I’ll need help. Also, I have a portable dissecting microscope, and I hope to have every other necessary item with me in the field, but it’ll be nice to have a fly lab that I can make use of for the day.

Yesterday, I met with Michael Turelli who was so incredibly helpful in helping me find drosopholists who can help me in the field. I have a good list of names, and I will be dropping his name when I’m asking these folks for help. I amazed at how few people know anything about the natural history of the fruit fly. It seems to me that if you want to study insect ecology, well, you might as well study the ecology of the insect about which we know more than any other! I don’t think they’re completely intractable as field subjects, they are cosmopolitan, and they exhibit niche specialization that puts finches and cichlids to shame. Oh well, it’s not like I’m going to trade in the pipette and computer for a Westy, a good net, and a notepad anytime soon. . . Probably not, anyway.

decisions, decisions…

I met with Jonathan today to talk about my future. It went well, I think. I don’t have to grab some crappy piece of the GEBA pie. I might be able to work on Drosophila gut bugs after all, or I might do more with metagenomic simulations. I’ll have to flesh that idea out a little more, but like I said, I do like metagenomics. And, I like the fact that I can sit down over a long weekend and read the entire body of metagenomics literature. Maybe I’ll do that this weekend… um, no. I’ll be wakeboarding and barbecuing!

Now, I’m going to start writing up the simulation project. I’d like to have that finished before classes start (that’s late September.) Speaking of classes, I’ve narrowed down my rotation options to David Mills, Scott Dawson, Ian Korf (if I can go with non-micro faculty) and Katie Pollard (ditto). If I can’t choose faculty outside of the MGG, then I’ll ask Mitch Singer and Kate Scow.


I’ve agreed to change my primary focus for my PhD project. Instead of developing the Drosophila gut microbiome as a model system to study the interaction of microbial communities with their environments/hosts, I’m going to do something else. So much for having a year’s head start on my dissertation research. Oh well – I’m sure it’ll be for the best. And, it makes sense that if I’m going to remain employed at the JGI, that my PhD project should be related to DOE/JGI programs. I still want to do that “Drosophila project” though. Jonathan’s still interested in doing it, but we need to write a grant before we do much (any?) more. I think I’ll propose a meeting with Deborah and/or Artyom. Maybe we can all write the grant together.

I’m also working on this simulated environmental sample. That’s coming along well, but the thing that I like best about it is that it’ll have a small work:impact ratio. Make a few libraries, write a nice paper. Not a PhD project. I do like metagenomics, though.

So, that leaves GEBA, or Genomic Encyclopedia of Bacteria and Archaea. I must say, for the record, that I think it’s unfortunate that this particular acronym seems to be sticking. I like GEM, Genomic Encyclopedia of Microorganisms, MUCH better. Both because “gem” is easier on the ears and because I know they’re eventually going to be sequencing some small eukaryotic genomes under the GEBA umbrella.

Anyway, GEBA sounds like my nightmare version of a project: open-ended descriptive science, of which I feel no sense of ownership. And, no field work! I know that it will be good for my career and I know that there are a lot of interesting components. I just need to find my niche. Fortunately, I have chosen my advisor well, and I’m confident that we’ll figure it out.


I’ve got to decide in which labs to rotate this year. I figure I’ll keep track of my options here. I’m not sure if I should choose labs because I think they’re doing cool, interesting stuff or if I should choose labs because I think I might be able to learn a useful technique.

1. John Roth
I am particularly interested in his work on adaptive mutation.
2. Scott Dawson
He’s a super-nice guy, and he’ll teach me some useful microscopy stuff. And, more than one person said that I should do a rotation with him.
3. Mitch Singer
Myxococcus seems like a very cool organism. Mitch seems like a nice, enthusiastic guy.
4. Ian Korf
This seems like a no-brainer. Especially if I’m going to be working on the GEBA project.
5. Katie Pollard
Statistics is (are?) fun! (and useful)
6. David Mills
I love wine!
7. Artyom Kopp
I feel like this is cheating a little (because I’ve already been working with him.) But, this might be a nice way to keep working on Drosophila for a while.
8. Wolf-Dietrich Heyer
9. Stefan Wuertz
If I can do a rotation outside of Microbiology, then I should definitely talk to him!
10. Michael Syvanen
Horizontal gene transfer.
11. David Begun