James and the Giant Corn Genetics: Studying the Source Code of Nature

January 31, 2008

Arriving at Berkeley

Filed under: University Visits — Tags: , , , — James @ 7:13 pm

I’ve arrived at the Berkeley City Club , and pretty soon will be going over to a lecture on campus before dinner. Meet another student from Cornell, and she’ll be putting pictures up on facebook, so I should have some visual aids after the fact. So far San Fransisco looks grey and foggy, but hopefully that will improve over the weekend. I’m really looking forward to interviews tomorrow, one of the advantages of Berkeley is that the department is big enough there are lots of different people doing research I’m interested in. 


The afternoon talk we went to (quickly):


Enriched amounts of C14 from nuclear testing in the 1950s provide a way of determining how long it takes carbon to cycle through into different parts of the ocean. Obviously it takes a carbon a really long time to reach some deep sea carbon cycles, since atmospheric carbon for the 50s hasn’t made it there yet. 


They found a six gene operon which is sufficient to allow otherwise heterotrophic bacteria to make ATP (energy) from sunlight, using a protein called rhodopsin which is also the light sensing protein used in the rods and cones of our eyes. You can splice this single operon into something like E. Coli which doesn’t get any energy directly from light, and suddenly that bacteria is capable of photosynthesis. The speaker has also found evidence that this operon has been taken up, as a unit into new, previously non-photosynthetic species in the wild. That was definitely the most exciting part of the talk for me


All in all, definitely worth getting soaking wet for. (I forgot to pack an umbrella when I as leaving at 4 am this morning.) Hopefully tomorrow is less rainy.

A Grim Beginning

Filed under: University Visits — Tags: , , , — James @ 3:28 am

A least my bad lucks are overlapping rather than combining additively or multiplicatively. 10 minutes before I was supposed to leave my apartment (at 4 AM) I thought to check my camera which I had thought was suffering from uncharged batteries and for which I had bought a new charger so I could photograph this visit. Unfortunately it appears the problem was more severe than a dead battery, and so I shall have no pictures of Berkeley, and when I get home I’ll have to figure out if the issue is repairable or if I need a new camera. The end result of this was that I was late arriving at the airport for my 6 am flight. They’re recommending two hours even for domestic flights now. But of course no one came out to man the ticket desk until 5 am, so I ended up spending extra time at home instead of waiting in an empty airport. Anyway, next post should be from sunny california. But you’ll have to rely on my descriptive prose instead of photos. -James 

January 18, 2008

The Day of the Thousand Interviews

Filed under: University Visits — Tags: , , , , — James @ 9:04 pm

Well five actually, but everything in due course.

Actually I’m just going to hit the major high lights:

The computer support they’ve got is amazing. On our tour of one of the facilities we walked into a room built for pure computational biologists. There where giant metal sleeves of cables running up from the center of every table surface, and looking up I saw giant bundles of ethernet cables running overhead. The only word that comes to mind is awesome.

Plenty of growth chambers and greenhouses of course.

I learned a lot about soybeans. Which was good. I got something to call my interest: crop genomics.

At the poster session they had this evening I met a guy who was working with wild rice, which is only in the earliest stages of domestication. The two things that struck me where the creativity he was forced into, given the extremely limited resources the government provides for such a small crop, and the fact that a big percentage of the money he gets comes from the wild rice growers themselves, and in return he goes out and meets with the grower association. He’s only of literally four people doing work in wild rice and the only molecular biologist. So it was really cool to talk to him.

Coolest Title I’ve ever heard of: Lichenologist (The Lichens that grown on rocks and trees, not the werewolves in Underworld)

Saddest realization: Not only is it a lot more work to cross soybeans than corn, but after you’ve made that cross, you get MAYBE 5 seeds. Not the 50-200 you’d normally get from an ear of corn. It seems to me that would change the way you’d have to do experiments in all sorts of ways, though I’m not having a lot of success thinking of what they are yet.

First Night In Minneapolis

Filed under: University Visits — Tags: , , , — James @ 2:38 pm

Arrived at University of Minnesota. Today was within the range of cold I’m used to back home, but on Saturday, the day I’m leaving, the high temperature is a negative number. 

My planned route to the hotel where they are putting us up turned out to have me crossing the bridge that collapsed last summer. I hadn’t realized the hotel was on the other side of the river, so I ended up driving circles through down town Minneapolis for a while as traffic began to surge towards the 5 o’clock rush hour. But I finally found the hotel and burst in just in time to catch the shuttle to campus. I also got a surprise, two of the people from the summer internship program at Danforth are interviewing with me. I suppose if I’d thought about it, that would have made sense, but I didn’t, so it was a complete surprise to be greeted by name as a dove headfirst into the hotel.

Anyway, the only event tonight was a combined dinner between Plant Biological Science, Applied Plant Science, and Plant Pathology. Lots of awkward mingling. As one girl I met pointed out, most people who study plants tend to be shy by nature. But at least that meant it was a level playing field. If there had been pre-med and business students thrown into the mix, all us plant science people would probably be huddled in the corner (by the palm tree, of course). I also met a number of PBS students who are very interested in ecology and disturbed ecosystems. Which I guess makes sense, since the leader of the program says PBS students everything from atoms to the entire planet.

On the ride back to the hotel, I talked to another interviewee who had corned some grad students over dinner to ask about housing costs, rents are apparently pretty reasonable in St. Lous (edit: St. Paul I mean), and with the way the housing market is going, some grad students are actually buying houses! Which is not something I would have expected to be able to do on a graduate stipend, but is definitely an…interesting idea. Anyway, tomorrow I meet with faculty so I should be heading to sleep, as I’ve been told on good authority the one surefire way to blow an interview is to fall asleep during it. 

January 15, 2008

Creative Free Stuff

Filed under: Uncategorized — Tags: , — James @ 4:42 pm

I’m still at my parents, and my dad just got home from back to back conferences in San Diego and New Orleans. He brought back a number of free give aways although my favorite for creativity is a shot-glass attached to a lanyard. I guess if you wore it at parties you wouldn’t have to worry about losing it when you’re falling down drunk?Anyway, tomorrow I’ll be making sure all the electronics my parents have added are in good shape (hopefully the last network adaptor will arrive tomorrow), and taking care of my car, then on Thursday it’s off to St. Paul for the weekend before heading back to class.

I’m here

Filed under: Uncategorized — James @ 12:52 am

I’ve just finished moving various files from the site I was testing them on to my new domain. Maybe it all looks cheesy to you, but I LIKE cheesy. 

Powered by WordPress