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

July 20, 2008

Rhubarb

Filed under: Uncategorized — James @ 7:26 pm

Safety Note: It should be remembered that the leaves of rhubarb should not be eaten, only the stalks. (Also deadly nightshade is also not to be eaten, as it is, in fact, deadly.)

Off the top of my head, here’s a list of the species I’d most like to study:
1. Corn – couldn’t you guess?
2. Bamboo – useful, exotic, and enough like corn that my previous experience would be useful
3. Sorghum – it’s hardier than corn, and its roots produce chemicals that kill off competing plants, how cool is that?
4. Deadly nightshade – plenty of genetic resources being developed in other Solanaceous species like tomato and potato and come on it’s DEADLY NIGHTSHADE!
5. Rhubarb – What’s not to like about a species known as “the pie plant,” and nobody’s done anything with its genetics (based on google searches for rhubarb + gene and rhubarb + genome) so I’d be in “here there be dragons” territory.

Since nothing is known about the genetics of rhubarb, today’s post will instead focus on the eating of rhubarb.
Chopped rhubarb
First chop your rhubarb stalks into one inch or shorter lengths. This is best done with a big knife and a fair bit of force, otherwise you won’t cut through the bottom fiberous skin.
Combine Rhubarb and Sugar
Add sugar. Lots of sugar. Aim for 25-35% of your rhubarb volume. What you didn’t expect me to be explaining how to make something healthy did you?
Let it sit
As you let the mixture of sugar and rhubarb sit, the sugar will draw moisture out of the rhubarb, which is why you don’t have to add any water.
Stewed Rhubarb
Yeah, I know it looks like Indian food, but it’s tasty and delicious in an entirely different way from how Indian food is tasty and delicious. Eat straight, or on top of ice cream, or any other way you’d like. For an actual rhubarb pie the process is essentially the same. Remember to replace the pot I used with a pie crust!

This post was the result of the sad discovery that there are people who’ve lived their entire lives in Iowa without tasting this delicious and enigmatic species.

July 6, 2008

Birthday Post 2008

Filed under: Uncategorized — James @ 5:59 pm

Once more I find myself mostly satisfied with the year, now past. I might actually be making a habit of this, but don’t jinx it. 

I got into a very challenging grad program, which I’m thrilled about starting in the fall. Given the local cost of living I may have to live on rice, beans, and ramen for five years. Fortunately my parents gave me a rice cooker and mini-crockpot for my birthday, which can been used to prepare the first two more easily, and it’d be hard to make the third (ramen) any easier to prepare than it already is.

I finished up at Cornell, if not with flying colors, at at least close to them. (Editor’s note: What’s close to flying colors? Gliding/hopping colors? Flying shades of grey?) The graph of my GPA by semester forms a nice U shape and a U definitely beats a \ shape.

To celebrate my suriviving another year on this planet, I had pizza and cake with family, followed by monty burgers, and the until now mythical monty-nator*, with close friends of many years. None of us got through even two burgers, and everyone was falling asleep by eleven-thirty, driving home the point that we’re not teenagers anymore.

*monty-nator: A monty burger (that is a burger prepared by a monty) wrapped in bacon, beer battered, and deep fat fried. Until recently the monty-nator existed only in theory rather like the Higgs boson.

(credit to monty for catching a typo.)

Remaining goals this summer:

1. Discover something cool (and ideally also publishable) about ultraconserved regions in monocots.

2. Assemble new energy effiecent ubuntu server and get software opperational, so I’ll be able to keep playing with the cammand line after I leave the lab this summer, and not pay huge energy bills to make my files constantly avaliable to my XBMC. <- XBMC is a great way to increase your stock with roommates. 

3. See the movies WALL-E and Hancock.

4. Do at least one thing unusual enough I’ll be able to use it as a topic of last resort when meeting people at Berkeley. (Basically what I was able to do with having gone sky diving my junior year of college.)

5. Find out what the genetic aptitude of the monty clan for producing tasty food can do when applied to baked goods.

June 27, 2008

Work, Class, and Dreams of Cake-Shakes

Filed under: Uncategorized — Tags: , , , — James @ 5:33 pm

Two years ago, I said the most fun I’d ever had while getting paid was the afternoon I spent doing sequence analysis for a seed company while listening to female fronted metal music. Well I’ve earned more money and had more fun since then, but there’s still something about working at a speed limited only by your own ability to think, while listening to a song like “Ice Queen.” I’ve been working on an computational genomics project in the lab, which means I’ve been coding and analyzing to Within Temptation and Leaves’ Eyes all week. The nice thing is that when I make a mistake with working on the computer it usually takes me a few minutes to correct it. Working in a wetlab a simple mistake could close me anywhere from an hour (I forgot to add something to a PCR reaction) to two weeks (I grew seedlings, harvested their tissue at the right age, extracted RNA, and then somehow let the RNA degrade to uselessness). So that’s the good news. The bad news is that I make a lot more mistakes working with the computer. But I’m getting better.

And a lot of the credit goes to the guy I’m working for, who has given me a project that was right on the edge of my ability and then known when to throw me a life preserver and when to let me sink or swim on my own. It means I’m producing results more slowly than I would have on a project more in my area of my experience, but I’m sitting right in the optimal part of the learning curve.

The two weeks of class before this were very instructional. We learned everything from R (A mathematical computer language that does a lot of the same stuff as matlab, only instead of costing hundreds of dollars it’s free), to machine learning algorithms (not as cool as they sound, but still plenty cool), to online annotation of genomes (it’s crowd sourcing for geneticists, but do all the geneticists in the world constitute a big enough crowd to be useful?).

What sounds like the lone surviving toad (apparently the new cat doesn’t turn his nose up at them like that old one) is singing in the pond out back. 

There was another mention of cake shakes this weekend (possibly tied to monty burgers) but I’ll have to wait and see what happens.

June 14, 2008

Floods of ’08

Filed under: Uncategorized — James @ 6:21 am

I’m perfectly safe ISU isn’t in the of the cities being hit hardest by the floods. University of Iowa on the other hand is in a lot of trouble. The friend I went out to visit in Iowa City a couple of weeks ago was evacuated from his dorm a week ago, and today the University announced they were shutting down for at least a week while workers fought to protect the university hospitals where surgeries were ongoing and rescue books from the university libraries. The east and west halves of the city are effectively cut off from each other, and emergency personnel divided on both sides since they won’t be able to respond emergencies on the other side. 

The worst hit is probably Cedar Rapids. They’ve lost almost all their drinking water, electricity is out for thousands and ten thousand have been evacuated from flooded portions of the city. A railroad bridge loaded down with train cars full of stone (to hold it down) was pushed off and floated away down river.

Most hit stories on the website of the Des Moines register:

Note stories #1 and #2 on that list. When I got the paper this morning the worst had past for Des Moines, but this morning the river broke through one of the levees built to hold it back after the floods of 1993 and water started flowing into down town Des Moines.

Lost of people have lost their homes. At the same time more than twenty percent of our crop acreage is just gone, and the remaining portions of fields will potentially be even less resistant to insects, fungal infections, and generally far more scraggly looking plants than would have been the case otherwise, so expect to see a substantially reduced harvest in the fall with increase more increases in the price of corn following.

February 3, 2008

Wrap Up In Berkeley

Filed under: Uncategorized — James @ 9:49 am

(Once more written last night, posted this morning) 

Done, coming home. Today was exhausting, if less intellectually stimulating than yesterday. Wine tasting. Indian dinner. Very sedate house party hosted by one of the grad students. Tomorrow we fly home.

 

The Indian dinner was nice because I got to chat with more of the grad students in a closer to one on one setting. There were five of them and only three of us.

 

Strangest pronouncement from an employee at a winery: “Now you’re going to find this next vintage as a kind of funky barnyard taste.”

 

I still can’t get used to palm trees. I’ve seen them in movies, but then again, I’ve seen velociraptors in movies too, and in my mind they both have about equal business showing up in the real world where people go about their daily business.

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. 

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