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

December 3, 2009

Make Sure Your Voice is Heard

Filed under: agriculture,Campus Life,Feeding the world,Politics — James @ 9:51 pm

Another positive side effect of extending my stay in Iowa for another week (besides having the chance to work from a room with a view), was getting the chance to see the Pamela Ronald and Raoul Adamchak give a presentation on the same themes are their book “Tomorrow’s Table” here on campus (I’ve reviewed the book itself).

Pamela Ronald is actually going to be talking in Berkeley late next month, but, in addition to a sneak peak of the presentation (which was really good) listening the the question session following their talk was a great chance to resample the perspective of the other major group involved in the debate on genetic engineering (besides anti-gmo activists, corporate public relations people, and plant scientists like me), farmers and agronomists.

What Pamela and Raoul advocate, distilled down to a single phrase, is agriculture utilizing “the best technology and the best practices.” The best technology is pretty clearly going to incorporate at least some genetically engineered traits, but the best farming practices will definitely incorporate approaches from organic agriculture. (more…)

October 6, 2009

Practice Talk

Filed under: biology,Campus Life — James @ 7:05 pm

For my teaching assistant training class we have to give half hour presentations. I just finished mine and I’m SO glad I held my own against the person who went before me. He had the advantage of talking about ecology, which usually is better at engaging the audience, and has a polished powerpoint presentation. My talk was basically an expanded version of Phylogeny of Pineapple, a further explanation of awesomeness.

People seemed genuinely engaged and the feedback after the talk was positive. Whenever phylogeny and genomics can go up against biodiversity and ecosystem services, and not be humiliatingly crushed is a victory for all of us.

No offense to ecologists, you guy do exciting research and I love getting the chance to sit in on your talks, it’s just nice when we plant biologists can get attention too.

September 30, 2009

Driving home how fortunate I am

Filed under: Campus Life,Fun With Numbers — James @ 5:24 am

According to this report (warning link is a PDF): 34% of workers under 35 still live with their parents. 52% of those under 35 and making less than $30,000 a year (me). Now from the way the statistic is phrased I assume that it includes teenagers with jobs, and excludes college kids without jobs. Even with those two caveats, it’s a frightening number.

Makes me grateful to be living in the apartment I share with only one roommate, noisy neighbors and all. It’s scary to realize how much of my generation is not so fortunate.

September 1, 2009

Assorted Updates

Filed under: Campus Life — James @ 5:27 pm

So it’s been a couple of weeks since I’ve updated. In that time I’ve:

Been back to Iowa for a few days where I feasted on giant hamburgers and saw a friend’s new house and kitten and another friend’s duplex. Enough to make a guy feel like he’s falling behind.

Bought and assembled a bicycle! The hardest part was setting the brakes properly. Since then I’ve been building up from a fifteen foot ride, to about 1.7 miles up a very slight incline and back again. Keep in mind I hadn’t ridden a bike since I got my drivers license back in 2001. That’s eight years, a major fraction of my life.

Had class start out here. It doesn’t really impact me much except there are a lot more people on campus.

Relatedly, the new first year students arrived. A smaller group than my year, they all seem frighteningly competent. At least three, possibly four, of the five new plant grads already have experience programming. They went to more prestigious schools. They’re way better about picking the best professors to rotate with than my class was when we just started out. I wish them all the best of luck.

Inherited an awesome new workstation in lab. Quad-core-dual-processor for a total of eight cores, dual monitors, running Ubuntu (of course), and I finally has a reason to use digital blasphemy’s multi-screen resolutions. Means I’m having to learn more about multithreading my scripts to take advantage of the power have available.

Still working on my post of basic genetics.

November 17, 2008

A Good Day

Filed under: Campus Life,Electronics,research stories — James @ 9:16 pm

I got up at 7 am this morning and got to work by eight.

I wore real shoes (not flip-flops) for one of the first times since I moved to Berkeley.

I work in a goverment building, with sign in sheets, and ID badges, and filters on the internet.

I didn’t even get the chance to talk to my new PI today, but I had the e-mail he’d sent me about my rotation project, so rather than sit around and waste time I started to work on it.

Did you know FT has 13 homologs in rice? And I found even more homologs in maize and mapped them on to the tree of rice genes using reciprical blasting.

The other people in this lab are really nice too. Two post-docs and one other grad student.

When I got home I realized I was babbling at my roommate about my exciting first day. We tend to be introverted around the apartment most of the time. I hope she doesn’t think I’m going insane.

To celebrate I cooked delicious pseudo-monty burgers (two plain patties left over from stuffed burgers on saturday, fried in a pan with a whole lot of extra spices.)

I also got an internet server working on my low power linux computer! It required a bit of tinkering to get around using the standard http port (most ISPs block connections on this port for residential costumers to discourage people from hosting web pages at home (like I just did!)). The page itself is just a proof of concept… I still haven’t figured out what I want to host at home (rather than using the hosting account I use for this blog) but it’s another advantage of an always on computer.

And for the record…I was able to bypass the filters at work. There’s no reason to, since I really don’t need access to facebook at work, but the point is, I can. And apparently people there have been trying to for over a year. (Some people really need their facebook.)

October 23, 2008

Addicted to Election News

Filed under: Campus Life — James @ 8:03 am


Daily schedule:

October 3, 2008

Weekend Update

Filed under: Campus Life,research stories — James @ 8:24 pm

It’s been a long week. I’ve been doing a lot more lab work this week (which has been great!) as I’ve learned more about the lab, and am able to work longer without having to ask questions. Coursework has also gotten more intense this week. We finished up our module on Genetics and Development on Tuesday, and started Computational Biology on Thursday.

So now I’m relaxing on the futon watching the Discovery Channel documentary on the frozen baby mammoth. They’ve got a big machine that takes the tissue down to -140 and grinds it automatically. I’m envious. But they’re using the same PCR machine I was using this week! Now on to 454 sequencing of the mammoth genome! It’s a hokey documentary (they keep having CGI mammoths wander into their interviews with scientists), but I’m enjoying it.

Hope to return to the Berkeley farmers market tomorrow. Maybe there will be a new mystery vegetable tomorrow.

October 1, 2008

Who Knew

Filed under: Campus Life — James @ 8:38 am

Apparently the year before I applied, the ENTIRE Stanford Biology department received over 400 applicants for six grad student slots.

Seems like it would be kind of lonely to be a plant person there. I’m glad I’m at Berkeley. There were eight grad students admitted in the plant program alone, and between PMB (Plant and Microbial Biology), MCB (Molecular and Cellular Biology), ESPM (Enviromental Science, Policy, and Management), IB (Integrated Biology), BioEngineering and any other departments I’ve forgotten there must be over two hundred new bio grad students this year.

September 7, 2008

First Retreat

Filed under: Campus Life,Recreational Travel — James @ 11:07 pm

The department gathered in Monterey (home of the apparently famous pebble beach golf course) to discuss science and meet/embarrass the new grad students.

Highlights (in no particular order):

The people who study magnetic bactera are really enthusiastic about the science they’re doing. The logic regarding how the bacteria are gaining an advantage by producing magnetic crystals seems a little hazy to me, although I’m not a microbiologist. But whatever the reason, the fact that they are is really cool.

Huge studies looking at the linkages between alleles of genes and the effects of drugs in humans. These are pure associate mapping studies, since you can’t do any controlled mating. Thousands or tens of thousands of subjects from drug studies. Convincing results that you can tie genetic data to drugs have no effect, enhanced effects or negative effects. The problem is that you can’t do anything cool about it. You can make more people take prevenative drugs. But you can’t introgress beneficial alleles into the rest of the population. Or make a transgenic line to test for complementation. This is why I work on plants.

The fields surrounding Gilroy, California produce some rediculus fraction of the total garlic crop in the US. The town features such cullinary delights as garlic flavored gum and garlic flavored ice cream as well as hosting an annual garlic festival, at which they crown the Gilroy Garlic Queen. We were told we’d be able to smell garlic just driving through on the highway and believe it or not we could.

Bonfires on the beach of the pacific ocean both nights. I haven’t seen the coast in daylight as of yet. But a good time was had by all. I was inducted into the secret society of grad students and given the sacred position of “fire bringer.” Translation: one of the graduating students handed me a box of matches and said: “ok, now it’s your responsibility to always remember to bring these.”

August 24, 2008

A weekend in the bay area

Filed under: Campus Life,Recreational Travel — James @ 9:50 pm

On Saturday visited SF with three of the other new students. It’s remarkably simple to get there on the subway. Saw the tail end of one of the famous farmers markets, and walked along the city near the north coast. Briefly visited pier 39 and saw more than a hundred sea lions there. A little farther along the coast a restored sailing ship was tied up to a dock. Constant stream of oil tankers and container ships into and out of the bay.

Walking back we cut through the city. Some streets are steep enough the adjacent sidewalks have been replaced by stairs. Chinatown seemed nice. As did Union square. Overall it’s a very different impression from my one evening in New York City.

Today my main accomplishment was making it to Target through back-to-school sunday traffic to purchase a microwave and enough food to last me another few days. The rest of the day was intended for quite reading, a plan that was foiled by the minor music festival held outside this evening that made it too loud within the apartment to hold a conversation on the phone without shouting.

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