November 29, 2003

Coolest. Educational. Toy. EVAR.

Posted on 08:37 PM
November 26, 2003
Dumb Waiters

Have I mentioned before just how much I love zombies?

In other news, I've been listening to The Psychedelic Furs an awful lot when at home and The Beastie Boys' Paul's Boutique when at work. It's an interesting combination, but not for everyone. Possibly not even for me.

Posted on 10:59 PM
November 25, 2003

Today was truly a fantastic day. Please pardon me while I geek out with a story.

I've been working to solve the structure of one particular protein since May. Before that, three separate rotation students and a postdoc put three years of manpower into the project.
As you may remember from my last post, I spent midnight to 6am at the Advanced Light Source collecting data on the umpteenth heavy-metal soaks for these crystals. After halfway processing most of the data from Monday's synchrotron trip, I was mighty discouraged, since none of the data looked promising. However, I started one more computing job before heading home to get some sleep.
Today I went into the lab thinking dark thoughts and trying to plan the next set of experiments. I was actually halfway through making up some solutions for an entirely new set of gold and platinum derivatizations when someone asked me how the data looked. Suddenly, I was reminded of the computational experiment I had set running before I left. I didn't really think it had worked, but the guy I was talking to wanted to take a look, so I trudged out to the computer room with him. The first thing we brought up was the initial electron density map from the last-minute job.

SHAZAM. A perfect alpha helix strared back at us.

Over the last several months my project has become infamous as the structure that (inexplicably) couldn't be solved. Take that, Laue!

Posted on 09:47 PM
November 24, 2003

Saw Matrix Revolutions this weekend with the Berger Lab crew and Friends. I wasn't a fan. Ate far too much delicious Thai food afterwards. I was a fan.
Instead of being home in my nice warm bed with Dianna, I'm at the ALS getting shafted by my crystals. The damn things diffract well, but I can't get any goddamn metals to bind with high occupancy. Someone shut off the jury-rigged pencil-bot, too, so there's not even mechanical hijiinks to keep me awake.

Oops. Almost time to get the next crystal ready for the beam. 45 minutes until someone comes to replace me on this shift. I'm counting every second.

Posted on 05:16 AM
November 15, 2003

Today I had a rather surreal experience. I decided to go get some coffee at a local cafe, and as I stepped outside I glanced at the sky and drenched trees I mused, "Wow....Berkeley looks a lot like Seattle when it's wet". No sooner had I thought this, than I noticed twenty people wearing the purple and gold of the University of Washington Huskies walking up the sidewalk. After about ten seconds of shock and bewilderment at my abilities to transport Seattle into Northern California, I realized that today's football game is Cal vs UW. I'm a little disappointed in my lack of superhuman mental powers, but I think I'll get over it.

Posted on 02:09 PM
November 07, 2003

Scientist uses loaded words, biased reporting, and outright falsehoods to misrepresent the truth. No one is surprised.

Gene recently linked to a Harper's article titled, "Unraveling the DNA myth: the spurious foundation of genetic engineering". In short, the article is absolute crap. Complete and utter nonsense. Which is inexcusable, because the author, Barry Commoner, is a biologist.

The article itself is 10 pages long, and it would take a similar amount of space for me to point out everything that is wrong with it. But let me summarize:

  1. "Known to molecular biologists as the 'central dogma,' the premise assumes that an organism's genome--its total complement of DNA genes--should fully account for its characteristic assemblage of inherited traits."
    WRONG. Absolutely, incredibly, inexcusably wrong. The central dogma states that DNA is read and used as a template to make RNA, which is then read and used as a template to make protein. But the dogma also recognizes that all manner of weird shit can take place between DNA (info) and protein (machine). To say anything else is embellishment and misinterpretation. The central dogma is one of the first things Freshman biology students learn. And somehow a career biologist managed to get it wrong. This leads me to....

  2. (paraphrasing) "Everyone was surprised when they found out that humans and flies had a similar number of genes, and now biologists don't know what to do".
    What the fuck is this guy thinking? We knew that the link between complexity and amount of genetic info was tenuous at best years before the various genome projects were underway. Any biologist who expected one gene to code for one protein has been living under a rock for the last decade. As for the idea that alternative splicing is a death-blow to the central dogma....that's the biggest load of crap I've ever heard in my life. It's a death-blow to Barry Commoner's incorrect statement of the central dogma. But it's easy to deal death-blows to straw men.

  3. "In genetic engineering it is assumed, without adequate experimental proof, that a bacterial gene for an insecticidal protein, for example, transferred to a corn plant, will produce precisely that protein and nothing else. Yet in that alien genetic environment, alternative splicing of the bacterial gene might give rise to multiple variants of the intended protein--or even to proteins bearing little structural relationship to the original one, with unpredictable effects on ecosystems and human health."
    Fuck you, Barry Commons. Fuck you. Stop assuming that the average reader will just nod and quote you at their next dinner party without worrying about whether or not you're actually correct. Splicing is caused by specific sequences at intron-exon junctions. Show me those sequences in bacterial genes, and I'll give you the nobel prize. They don't exist. When eukaryotic genes are spliced, it is because part of the gene reads, "splice me here in X number of ways, depending on what other signals are in the cell". To the best of my knowledge, prokaryotic genes don't contain this information. Just because Barry Commons says they do, doesn't make it true. Wringing your hands over the fantasies of the village idiot is not worthwhile.

I think that's all I'll say about this. Everyone has probably already lost interest, anyway. But please, if you think GMOs are a bad idea, don't quote Barry Commons to support your position. There are several reasons you might oppose genetic engineering. But outright falsehoods are not good reasons.

Posted on 01:10 PM
November 05, 2003
Vampire Can Mating Oven

Today the mailman gifted me with something wonderful: Camper Van Beethoven's Cigarettes and Carrot Juice box set. This has got to be the best musical deal in existence. Five (5) full-albums for thirty (30) dollars. That's six (8) dollars an album. It really doesn't get any better than that.

Dianna's not so excited, though. She's especially unexcited about the bizarre screechiness featured during "9 of Disks" or "Payed Vacation: Greece".

My kitten hasn't moved in three (18) hours. I think she's asleep. But it's also possible that she's turned into a very fuzzy (2) statue.

Posted on 10:23 PM
November 01, 2003
Juicy Fruit

This morning (the day after Halloween) was surreally peaceful. I woke up at 6 a.m. to go to the Advanced Light Source and shoot some crystals, and discovered an empty Berkeley. The streets were almost completely empty, as if half of the Bay Area had suddenly disappeared in the night. Then again, I haven't heard anything about the Castro Halloween mobs yet, so maybe they have disappeared.

My morning was made even more surreal by the latest contraption the beamline scientists have come up with. As I set my bag down in front of the control computers, I noticed some movement out of the corner of my eye. It seems those wacky techies have built an articulated robot arm to automate crystal handling. Except, in true beamline style, part of the robot is made of #2 pencils. There are experiments in other areas of the synchrotron that seem to be made entirely out of tinfoil. I find something intensely satisfying about coming into such an ultra-cool sci-fi environment and finding it held together by chewing gum.

Posted on 09:39 AM