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

October 28, 2008

What A Difference Four Years Makes

Filed under: Politics — James @ 9:35 am

“To Those Who Inquired:

This is a picture of me with my absentee ballot. Seconds later, I carried it down to RPU and put it in the mail. I’ve done what I can.

-James” (Nov. 1st, 2004)

I like the democrats chances a LOT more today than I did four years ago when I sent that fatalistic e-mail and that absentee ballot. And that’s even though they’ve lost my crucial swing state vote, as I’m now registered to vote in California, where the swing elections are on things like Prop 2 (Increased rights for farm animals) and Prop 8 (Taking away the right of gay couples to marry).

Here’s my favorite* of the pro-prop 8 ads that have been running constantly in California.

This is essentially the same argument they used back home to fight the proposal to add sexual orientation the school’s anti-harassment policy: If you give these people legal recognition and protection, how can we teach our children they aren’t allowed to be gay?

*Wouldn’t this ad be more amusing if they cut out the guy in the middle and just had the mother daughter conversation set to the dramatic music from Jaws? “Dun dun dun dun dun”?

October 25, 2008

My District Back Home

Filed under: Uncategorized — James @ 5:52 pm

As if I needed another reason to regret having to register to vote in California…

A poll this week showed my former congressman Latham running within five percent of his challenger Becky Greenwald.

Of course my current congresswoman Barbara Lee, is a far more progressive legislator than either Latham or Greenwald, but she generally wins reelection with more than 80% of the vote.

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.

Addicted to Election News

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


Daily schedule:

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 20, 2008

2004 Results

Filed under: Politics — James @ 4:45 pm

I spent a while this weekend trying to find a record of the order that states were called in on election night in the 2004. I finally found a table of NBCs predictions, but it really didn’t have a lot of impact as a big chunk of text. Since I’ve been looking for an excuse to practice Perl (and as a completely unintended consequence put off homework) I set out to make a movie. In hindsight, counting all the time I spent debugging my own code, it would have been faster to produce each frame by hand…

Note that Kerry conceded and Bush was declared the winner at around 11:30 the next morning when the video stops. At that time the winners in four states remained unknown. (Iowa, Wisconsin, New Mexico, and New Hampshire.) 


October 18, 2008

Bios Drama

Filed under: Uncategorized — James @ 4:12 pm

Before my new processor even arrived I needed to upgrade software embedded in the motherboard in my linux computer (the BIOS) to be able to handle the new high tech processor I ordered.

It’s remarkably hard to upgrade the bios on your motherboard, when you don’t have a floppy or CD drive and are running linux. Some motherboard manufacturers make updates available in forms that run under Linux, and I’d highly recommend those brands to people looking to build a linux PC. Otherwise you’re stuck swapping HDs from your windows computer, which convinces windows that it’s been pirated, plus you’ll have to install the windows ethernet drivers for your computer to be able to access the bios update online, which (since you don’t have a CD drive or a working internet connection) requires a fair bit of work.

All in all, I see this as a vindication of my multi-computer policy as this required three in order to work properly: one to need updating, another to steal a hard drive with windows installed on it, and a third to remain functional for downloading drivers and saving them to flash drives which would then be accessed by the Frankenstein-ian hybrid I created.

Especially since somehow, in the processor of upgrading, I ended up with a “rogue anti-spyware” program on my windows hard drive (no idea how that happened) that proved so persistent that I was forced to reinstall windows from scratch before it would run again on my ACTUAL windows computer. 

Upgrade complete

Filed under: Electronics,Fun With Numbers — James @ 4:09 pm

You might recognize this computer:
Then again you might not. After all a black box isn’t very distinctive. Regardless, this is the central server of my home network. It stores 3.25 terabytes of data between internal and external hard drives, can serve video to any computer in the house, and is accessible via VNC or ssh anywhere in the world (that I can get internet access), and draws less electricity than the average lightbulb. And now, after the arrival of a gift and less than an hour’s work it’s more useful than ever.

As I outlined before, the main bottleneck I faced was processor speed. With the arrival of the components I’d talked about that bottleneck no longer exists! Everything happens blazingly fast. I can’t wait to try out WUBLAST on this new and improved machine. I want to build a private database of the rice, sorghum, maize, and brachypodium genomes (and platypus genome, why not?) all in one location.

The wonderful thing about doing bioinformatics, is that if you just feel like messing around and seeing what there is to find, it doesn’t take hundreds of dollars of reagents in a controlled lab environment with super expensive pieces of equipment.

But applications later, for now I just want to enjoy how cool it 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.

October 13, 2008

Angel Island Fire

Filed under: Uncategorized — James @ 9:33 am

Angel Island is in San Francisco Bay. And it’s burning.
11:23 PM
For the record, I can’t take credit for taking this picture myself.

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