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

January 26, 2009

Chinese New Year

Filed under: food,Photo Posts — James @ 2:32 pm

Lots of new photos up on Flickr. On Saturday I went down into San Francisco to see Chinatown in the weekend before Chinese New Year (which is today:  新年快乐 ! <– I theorize this means happy new year, given it’s appearance on so many people’s facebook statuses over the past few days) Lots of pictures.

That night we decided we wanted cake, and took advantage of the fact that I keep buying boxes of cake mix, even though I never get around to mixing them. Resulting in so much cake. Just to clarify, there are FOUR pans of cake in this photo:
Four Cakes

Work is going well. Only two weeks left in this rotation and I’m racing to have something to show for my three months of effort.

This is the year of the ox. The second time it’s come around since the year of the ox when I was born (which for those doing the math means I’ll be turning 24 all too soon.)

January 18, 2009


Filed under: Photo Posts,Plants,research stories — James @ 9:57 pm

Jamesandthegiantcorn turned one year old on thursday (and a good friend of mine turned 23 that same day). As it happens this will also be my 100th entry, I’ve averaged about two updates a week over the past year, which is pretty good given my previous experience with blogging. Without further ado, my 100th entry:

Brachypodium? What is it? Well it’s a grass species that looks like this:

 Brachypodium distachyon

I first mentioned it almost a year ago in an entry I posted during my interview weekend at berkeley:

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 brachypodium.” <– I’m better at remembing the names of new species of grass than of the people I meet who study them.

Obviously while I remembered the name, I did not learn the spelling. But since then I’ve learned a lot more about the species and why people study it. Brachypodium is a tiny temperate grass that is (like so many other species) an “emerging model organism.” That means people think studying brachypodium can teach us more about other species*, and are having brachypodium’s genome sequenced. Part of developing a useful genome is annotating genes, which is something I’ve been working on during my rotation.

*I would say the reasons its considered a good model are first that brachypodium is what arabidopsis (the first plant ever to have it’s genome sequence) would be if arabidopsis were a grass: a small plant with a small genome and a generation time of only six weeks (compared to 3-5 months for corn, or 15-20 years for humans). 2. It’s much more closely related to wheat than any other sequenced plant, and wheat could use better molecular resources.

Of the big five crops, rice, maize and sorghum as all getting their genomes sequenced. The two that aren’t are potato and wheat. Potato is tetraploid (where humans have two versions of every chromosome potatoes have four versions), and wheat is hexaploid (six versions of every chromosome!). Until sequencing and assembly technologies improve, the closest we can come to sequencing these vital crops is a related species with a more tractable genome (tomato for potato and brachypodium for wheat).

PS The new comment posted will be the fiftieth non-spam comment on this blog. A lot of milestones this week.

January 11, 2009

Vegetables and More

Filed under: Photo Posts,Plants — James @ 7:23 pm

I was originally going to post this yesterday afternoon, but instead I had a crises with my Linux box which I’ve just now resolved. I’m just lucky I bought so many 500 gig hard drives back in undergrad that I had an unused spare on hand when the Operating System drive in my computer suddenly went bad.

Anyway the point of my post was to draw your attention to the new pictures I’ve put up on Flickr of my expeditions into the world of vegetable buying. Be sure to especially check out the purple cauliflower (because that’s intrinsically cool) and the newest entry in the “name that mystery vegetable” contest:

Mystery Vegetable Episode 2

It was actually a lot of fun. I’ve been to the local farmers market a bunch of times. But it’s very expensive, and they’re openly opposed to people like me:

Sad Sign At Berkeley Farmers Market

So on Saturday my roommate took me up to the Monterey Market (which is on Monterey Street, not in the city a couple of hours away) which is just amazing.

Monterey Market

More fruit

My only real disappointment was that I finally found papayas from Hawaii (which is where virus resistant papayas were first introduced as a cure for the papaya ring spot virus that was ravaging the papaya farms) and they were organic. Of course it turns out I could have bought it anyway, as many organic papayas are now “contaminated” with the resistance gene (according to wikipedia) allowing organic cultivation to thrive in areas where the virus would otherwise make it unviable.

January 3, 2009

iPhones In Iowa

Filed under: food,Photo Posts,Recreational Travel — James @ 11:36 am

One of the gifts I received for Christmas this year was an iPhone. Well, actually a gift card for an iPhone, apple has become very picky about allowing anyone to purchase an iPhone without signing up for the service contract right there on the spot. (There’s so much demand for them in foreign countries where it hasn’t be introduced yet, and from people in the US who want to use iPhones on other carriers.)

Anyway, I finally purchased said iPhone at a nearby apple store in Berkeley (located as it happens in an open-air mall which is a much better idea in California than it is here in Iowa (with months of freezing winters and more months of blazing hot heat) yet they’re currently in the process of constructing such a structure in my hometown because open air malls are the “in thing.”) And it’s a good thing I did. It was a lifesaver during my delayed and re-routed trip home. Air travel is a lot less stressful and a lot less boring when you’re able to check and respond to e-mail and surf the web. Plus with a free app called stanza the iPhone makes a quite passable e-book reader.

Getting back into Iowa has been a lot of fun. Hickory Park would never survive in California, but I love it:

And it really is winter here:

Did I mention that with my iPhone, I can now upload geotagged photos (click through to flickr on this photo, and it’ll tell you where it was taken along with a link to display the exact location on yahoo maps):
Matthew with Athena

I am now in complete awe of my friend Ben’s ability with infants. If I ever am in a position where I’m going to be expected to take care of one myself, he’s the guy I’ll call for advice. His little niece is tiny (less than a month old) and smelly…
Monty with Inara

November 30, 2008

The True Goal of Thanksgiving Dinner

Filed under: Photo Posts — James @ 3:47 pm

Thanksgiving Tastyness
A late night snack consisting of a thanksgiving roll, turkey, and cranberry sauce. If your meal produced the leftovers requires to assemble this, your thanksgiving was officially a success ;).

November 26, 2008

California Gas

Filed under: Photo Posts — James @ 9:50 pm

What you are seeing is real. A gas station on my drive home from PGEC was selling gas at a 1.99 a gallon… in California! This depression/recession/economic ennui/whatever-else-you-want-to-call-it is not going to do good things for renewable fuels. (Though it may be good for the short term financial solvency of grad students on stipends.)

October 23, 2008

My Poor Pumpkin

Filed under: Photo Posts — James @ 8:06 pm

Rotten Pumpkin
I can home from the lab today to find the pumpkin we’d carved five days ago in this condition. This is either a result of buying pumpkins from organic vendors or (far more likely) the lack of the cool to cold fall weather that preserved jack-o-lanterns back home.

October 22, 2008


Filed under: Photo Posts,Plants — James @ 1:29 pm


Bottlebrush is one of the rare species of plant where a single apical meristem can produce flowers and then switch back to producing normal vegetative leaves. Also the genus is native to Australia so obviously its presence in California is a result of human intervention.

The red fibers that make up the majority of the flower are actually anthers (the male portion of the flower). The petals are almost vestigial, with the anthers taking over the petals’ normal function, attracting pollinators… though I don’t know what the pollinator of the bottlebrush is.

October 16, 2008

The same stuff as rainbows

Filed under: Photo Posts,Plants,research stories — Tags: , — James @ 5:40 pm

Thinning out my corn seedlings today I was struck by the fact that is:
Is made of the exact same stuff as this:

Plants may grow out of the soil, but when you’re holding a whole big mass of them, the weight in your hand came from nothing more than water, air, and light. The same stuff as rainbows.

I remember the first time I learned about that in high school biology. A guy in Europe weighted a pot full of dry soil, then planted a seed in it, watering only with distilled water. Over several years the seed grew into a large tree, which he finally uprooted, carefully rinsing off all the soil from the roots. After it had dried, he reweighed the soil, and found its mass almost identical to what it had been before he planted the tree. That very real, very solid, tree, made of nothing but water, air and sunlight.

September 9, 2008

Thank You All

Filed under: Photo Posts — Tags: , , — James @ 12:11 am

This one goes out to all of you who’ve made me tasty food.
My friends:

The girl I live with:

My girlfriend:

And my friend’s girlfriend:

Thanks also to my ex-girlfriends (food not pictured), my friend’s ex-girlfriend (food not pictured) and my girlfriend’s friend (additional pecan pie not pictured).

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