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

March 18, 2008

From the Hotel of Moose

Filed under: University Visits — Tags: , , — James @ 7:34 pm

Greetings from Colombia, Missouri. I’m here doing the absolute last of my college interviews. So far it’s going quite well. I met with a few faculty and had dinner at a Thai restaurant. I like spicy Indian food, spicy Thai food turned out to be a little more than I can handle comfortably. It’s a very different experience to be a single student visiting, vs one of a herd of students.  I like what I’ve seen of Colombia so far, and the plant program sounds quite strong, though I’ll be in a better position to comment on it after tomorrow. And to explain the title, the hotel they’ve put me up in has moose everywhere. Pictures on the doors to the rooms, in the lobby, there’s a big statue of one in a pond outside the front door, even the lamps next to the bed are in the shape of moose. 

February 22, 2008


Filed under: University Visits — James @ 8:12 pm

I arrived in Madison last night. This was definitely ones of the more relaxed visits I’ve been on. The first night I was on my own for dinner. In a strange city. Late at night. With no winter coat. So I ended up going down to the bar in the hotel and take a pizza back to my room to eat while watching the presidential debate.


Friday morning I had breakfast with a couple of people from one of the USDA labs on campus, and got the meet the other prospective student who was interviewing the same weekend. I was impressed by how easy it was to get people talking about. Not their own research, but things like the Sargrasso sea meta-genomics project. Some of the other schools I’ve visited, people would talk about their own research, but it was harder to innitiate a discussion of random science.


After breakfast I got a ride in a minivan to campus, where my first meeting was with a plant breeder who works on carrots and garlic. Did you realize that while the average american’s vitamin intake as a whole has gone down or stayed the same over the last fifty years, our vitamin A intake has actually increased mostly as a result of selection for darker orange carrots? Or that purple carrots (which express anthocyanins, the same compounds that make the bases of some corn stalks purple) are being considered as a source of long lasting purple organic dye for things like clothing? 


Then on to a woman who works on germ plasm enhancement in potato. Also a very exciting discussion. Given the ease of switching between diploid and tetraploid individuals, there’s a lot of stuff fun they can do with bringing in genes from wild relatives of the domestic potato. And it raises the potential for developing a potato with four-fold hybrid vigor by generating two diploid hybrids and then combining the two genomes by selecting for diploid gametes . But that’s a long way off. 


After that I meet (sequentially) with three people who do maize work. Also amazing, but not something I’ll be talking about as much here. The key phrase, which I think I should have engraved and hung above my desk is: “Twice as much corn is still twice as much corn.” The context being a discussion on the benefits of focusing on breeding corn to increase biomass, vs breeding corn which is more easily converted into cellulosic ethanol. The latter could always be made obsolete by a new technology for breaking down currently resistant compounds, but the former (say it along with me):


“Twice as much corn is still twice as much corn.”


Both a breakfast, lunch (which we had on campus in their cool looking new microbiology building) and dinner (at a place called Great Dane a microbrewery and restaurant, reminds me of a cross between Hickory Park and Old Main) I was struck by how into plants the graduate students in the program were. The shop talk wasn’t about molecular techniques or who got what grant a new machine that cost X thousand dollars, it was about the plants themselves. And because of that, it was easier and more fun for me to make conversation with people over meals.


So I keep thinking I know where I want to go, and then I visit another school and things get more complicated again. Fortunately this should be my last school visit. So now I get to fly home and bang my head against my desk until I come to a decision. 


For now, I shall lie back in my king-sized bed, and watch the newest episode of Stargate Atlantis on the 32 inch flat screen TV in my room. 😀 

February 14, 2008

Retrospective CSHL (part 3)

Filed under: University Visits — Tags: , , — James @ 1:42 pm

Saturday started out with another couple of interviews. Even with 20-30 minute interviews and no time built into the schedule for traveling between labs, they weren’t able to fit them all into one day. 


I should also mention that there are no room numbers at CSHL. Once I found the correct building I just stuck my head into a room and said, “Sorry to bother you, I’m looking for Dr. X’s office.” (I didn’t actually interview with anyone named Dr. X, but it would have been cool if I had.) This was actually good marketing for the organization, since every response I got to doing this was both polite and enthusiastic.


We had an enjoyable lunch where all the grad students and faculty ended up in one room and the interviewees in another. Not great for making a good impression, but it was fun to get to know the other people I was interviewing with better. And one of the pizza’s provided was covered in MEAT. Berkeley was a very vegetarian friendly campus, sometimes frustratingly so.


After lunch we got the tourist tour of CSHL. The first building was constructed as Origin of the Species was becoming popular. So people were starting to get very excited about the study of evolution and inheritance. But how do you study those things? They didn’t know anything about DNA. So one of the early things they studied was the way that embryos developed. And the easiest systems to study that in are fish, since it’s possible to observe the embryos in fish eggs develop without having to crack through a shell or dissect thousands of pregnant mice. Later as Mendel’s work was rediscovered by biologists CSHL moved on to breeding experiments, and then when the first genetic techniques were developed the exciting research moved to viruses, with the smallest genomes of any organism. We saw a gazebo on the waterfront with a sculpture of a virus on the roof. I’m told couples from the lab often get married under the virus…


Scary though of the day:

“The average person alive today is as likely to die in an airplane crash as a meteor impact.” 

February 13, 2008

Retrospective of CSHL (day 2)

Filed under: University Visits — Tags: , — James @ 8:20 pm

Ok so my laptop is back up and running at a reasonable speed after some RAM issues. I also have a working camera again, and, by cleaning under by bed, once more have the technology to transfer pictures from my camera phone to my computer. Which allows me to bring you this picture (click to see a larger version on flickr):


Dance of The Polypeptides  

So when last I checked in, I have just gotten through my first day at Cold Spring Harbor, and was facing a grueling day of interviews.


Well it was grueling. I met with more than three times the faculty I did at Berkeley, and all on these were one on one meetings, no being able to fade into the background of a group meeting. The other major different between Berkeley (as well as Minnesota) and Cold Spring Harbor as that at the former schools ask roughly the same number of people to interview as they’re planning to extend offers to. The result is that the interviews focus on learning about faculty’s research and lab management styles, while trying to avoid making any strong negative impressions. (For example, I was told a guy who feel asleep during an interview with faculty was not offered admission.)


In contrast, Cold Spring Harbor invites six times as many interviewees (spread over three weekends) as they would like to see in their entering class of graduate students. There were two kinds of meetings. Those with PIs who I’d either requested or how requested to meet with me, which were similar to my interviews at other institutions, and interviews with members of the admissions committee. And the two were marked identically on my schedule.


Unlike previous schools I actually had to sell myself during the interviews. It took me until about my third interview to adapt to the new dynamic.  Those interviews tended to focus on my own research as an undergrad, and fortunately I had several research projects to talk about, and (I hope) a good grasp of the greater context. First I’d explain what I’d done, then answer questions about why it was important, or why we’d used the techniques we used, or what have you. Towards the end I was actually starting to enjoy myself. Being able to talk about experiments that I was personally very interested in, to people who were both bright and well educated, but knew less than I did about the specific topic. There aren’t any plant PIs on the admissions committee, so I was mostly talking to people with backgrounds in cancer and neuro biology. So I also got to learn about subjects at adjoined on my own, but in which I had very little background.

February 7, 2008

Cold Spring Harbor Lab (Installment 1)

Filed under: University Visits — Tags: , , — James @ 10:31 pm

I’ve arrived in Cold Spring Harbor, and am writing this just after midnight.


Instead of staying up all night to catch a 6 am flight like I did to Berkeley, I was able to sleep in a little, drive to the airport at noon, and take a direct flight to NYC, where I and a fellow student were picked up by a driver waiting for us with a sign and driven out to CSHL. On the plane ride out I was seated next to two Cornell prospective investment bankers who were getting flown out for a sell weekend. (They’ve already been offered jobs and now the banks are flying them out again to wining and dine them in an attempt to influence their decision.) One was a fellow Iowans, which is cool, as there are something like 15 of us at Cornell. (Based on a very old facebook search.)


The first event this evening was a talk about the approach to graduate study at CSHL vs other places. It boils down to, getting classes out of the way the first semester, graduating in four years instead of 5-7, and giving the lucky few who get admitted lots of support in their living circumstances and learning, so that the students can focus on giving 150% to their research. For example the organization provides highly subsidized housing, and if will help you find non-lab housing if you want it, especially if you need room for a partner and/or children. 


Then we were matched up with our individual graduate student hosts and went out to dinner in a number of small groups. Mine was 50% current or former Cornell students. The highlight of dinner was a dessert called “King Kong,” which featured chocolate cake in the shape of the empire state building, lots of vanilla ice cream, strawberries, and sparklers. I wish I’d gotten a picture of it.


Came back to the CSHL bar and had a chance to grill grad students more thoroughly. Note that several of the grad students were running back to labs to set up, run, and image gels between beers.

February 2, 2008

Corn Mug!!!

Filed under: Free Stuff,University Visits — Tags: — James @ 10:44 am

I forgot to mention, at breakfast yesterday they gave us a little set of gifts all inside a PMB mug… made out of corn plastic! Also, there’s a key chain that’s a cube of clear plastic lights up and there’s a three-D model of DNA inside. So those were both cool.

The Second Night … In Berkeley

(This entry, and the previous one were written last night and posted this morning when I have internet access.) 


So after we were all done with interviews for the day, we hung out in the “grad pad” for about fourty minutes and I got to get to know some of the other people I was interviewing with better. One girl who was born in Iowa, but doesn’t live there anymore. Another from Texas A&M who knows Carlos (one of my roommates last summer). Another who graduated a semester early and moved from the west coast to the east coast to live with her boyfriend, now fiance who she met at a REU program. I’d estimate half the people interviewing are going to be graduating this spring and half have been out of school for some length of time already. 


In some ways I feel like one of the less qualified applicants. There are people who were first authors on papers as undergrads. My roommate is from Brown. As I mentioned previously, at the airport I met another girl from Cornell who’s also a Bio-Plant Science concentration (there are only like 10 of us at Cornell, and yet the two of us had to come all the way across the continent to meet each other). So it’s not like I have a monopoly on the Ivy League thing.


Anyway at six we walked over to a pot luck that was hosted at the house of some friend of one of the program organizers. Which was a really fancy place. (And as I found out last night, Berkeley allows the use of recruitment funds to buy alcohol, which is a no-go at some other schools.) It was good the get to talk to a bunch of the grad students in a less formal setting. Either the microbiology people (Berkeley combines micro and plant biology in one department) were a lot more outgoing than the plant people, or there were just a lot more of them there, since I always ended up in conversations with them, but it was still a good time. And then hours later, I got to get a ride back to the hotel in a compact car holding seven people. Which was definitely one of those experiences everyone should have in college. (At least I got to be one of the people donating laps instead of one of the people sitting on them.)

Another Day of 1000 Interviews

Filed under: University Visits — Tags: , , — James @ 10:33 am

(This entry, and the following one were written last night and are being posted today, now that I have the time to get internet access.) 


This time I have seven. Three with faculty, and four with the labs of absent professors. And I can honestly say that I walked out of each interview very excited about the science in that lab. Also, it was nice and sunny today which was a vast improvement on yesterday.


Very briefly, I interviewed with a guy who does phytochrome research, which is what my undergraduate research started out in, so I was able to talk intellegently about that, and he knew the guy I work for at school. The meeting was very VERY brief though, they drove us out to the PGEC for an hour and I was scheduled to meet with three groups during that time. The second woman I talked to studies the regulation of cell differentiation in meristems. If I was less tired I could talk about that in a lot more detail, but the sobering part was when I realized her research was behind about a third of what we had learned about shoot meristems in my plant development course last fall. But once more fascinating (I’ll be using that word a lot.) Then a meeting with a lab group whose PI wasn’t in town, but I thought they managed it quite well, some of their work ties in with the Ramosa mutants I worked with several summers ago, and it was, you guessed it, fascinating. Then it was back to Berkeley’s main campus for lunch and MORE interviews. I was fortunate in that most of the on campus people seem to be centered in one building, the microbiology people had to run around to a lot more buildings. 


Another thing that both I and a couple of the other people who are interviewing noticed was that the grad student’s here at Berkelely seem happy. I haven’t been to any schools where all the grad students seems depressed, but there does seem to be a lot of variation.


But my first interview of the afternoon was particularly exciting, I promise I’ll be very brief with the last three. It was with a woman who studies plant evolution in all sorts of REALLY weird species. Like cycads. Which are gynosperms (a group of non-flowering plants which include things like pine trees) which pollinate each other by using insects. The insects are drawn to both the male and female cycad cones. But the cones heat up on alternating schedules driving the insects out of male cones, where they’ve been coated in pollen, to the female cones, where they fertilize individual seeds.  (The fact that this plant is able to generate heat, vaguely like a warm blooded mammal is pretty cool in of itself.) And then we ended up in a discussion of how cycads may have more trouble spreading their seeds now that dinosaurs are extinct. So that was really cool. As I promised, I’ll mostly skip over the last three labs, not because I was any less fascinated, but because it’s harder to describe. An imprinting lab, a epigenetics lab, and an genomics/bioinformatics/evolution lab. In the last of the three we learned about how transposons can be “domesticated” and adapted to serve a purpose within the host species. The guy I was talking to claims that’s actually the origin of the immune system in animals. Complicated story there, I’ll try to explain it if anyone asks.


Best Metaphor: “Some labs are like viking ships and some labs are like dingies.” (And dingies are the good ones)


Most “I’m definitely a potential grad student” moment: 


“Um…wait…I can’t remember his name but he works on a species called bracopodia.” <– I’m better at remembing the names of new species of grass than of the people I meet who study them.

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 

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