Duke Gardens

Spring in NC. Pictures taken March 20, 2010









'The process is the outcome through which the outcome is the process.' -Unknown (Love life NOW!)

Phenix and a New Car

So I’ve has been very busy this past week; it was spring break. For me, all that meant is that I had no classes; I still had to go into lab. We had a very special week in lab as we hosted the Phenix conference. Phenix is software used in crystallographic structure refinement. The Richardson lab, of which I’m a member, is one of the developers of Phenix. The exciting aspect of the conference for me was that my code, that I wrote as an undergraduate (and am still developing), might be incorporated into the Phenix package!

The conference was great! I met a lot of awesome people from all over the USA and a few from Europe. We had developers and industry people there. The industry people were from a variety of drug companies. There were two industry people that worked in Copenhagen. Both were from Norway but understood me when I sang Happy Birthday in Danish. The conference was a time to cash in on free meals. We went to a different restaurant each night and had a variety of lunches each day. It was very busy as the earliest I got home was 9:30 between Sunday and Wednesday.

For the last couple of weeks I have been shopping around the Internet for a car. Last Saturday I decided to go look at two cars at a used car lot in Raleigh. The first car had a strange sound emanating from the engine while the second car smelled HORRIBLE. My roommate, Jeremy, then led me to the near by Honda dealer. We mainly looked at 2007 Accord lease buybacks. The top choice was an Accord with 3,900 miles on it, which was put on the lot the night before. The car was owned by a 92 year-old woman who had her license revoked with a year left on the lease. I wanted it but was beat to the punch by a couple that was trying to qualify for financing. So there was a possibility that I could still get the car. I had to wait until Monday to hear whether the car was mine. After a long weekend I received a phone call indicating that the couple didn’t qualify. A few hours later I was driving home my new car (see below).

That’s all for this week. Enjoy the pictures.

As you can see, Grandma did some contact parking.

My room mates. Oh ya, me and my new car are in there too.

My Lab Choice

The last two weeks have been rather uneventful; school, eat sleep, etc. I am wrapping up my third and final rotation this week. As such, it is time for me to choose a lab to do my dissertation work in (where I will spend the next 5+ years). I’ve made it pretty evident which lab I hope to join but had to jump through the hoops. Last Friday I officially asked Dave and Jane Richardson if I could join their lab. It took them less than a millisecond to answer in the affirmative. We had a great discussion! It will be an exciting, albeit a very challenging, 5 years. In laymen terms, and a rather crude analogy, I am going to be resolving a clear picture from a low-resolution rendition of the picture. Of course this simply means I will be attempting to improve methodologies of low-resolution x-ray crystallography protein structure building and refinement.


The reason for the Bill Nye picture: So, one of the hoops that I had to jump through is to turn in a sheet upon which I request my first a second choice for the lab that I want to join. As explained above, I had already discussed joining the Richardson lab, so there was no reason for a second lab choice. Naturally, I had to think of something smart to put on this official document. After much consideration, I chose Bill Nye.


I did finally go on a date Saturday. It was pretty low-key. We walked to TGI Friday’s then went back to her dorm where we talked a tad bit longer. It was a great date; since we walked to the restaurant we had a lot of time to talk. She is an electrical engineer undergraduate who likes reading and taekwondo. There is going to be a second date, where we will actually do something other than eat.


I have gone to a few basketball games here at Duke. The student fans are notorious for being crazy and loud. After going to a few games I can confidently say they have nothing on Utah State fans. While the students here are loud, the students in the Spectrum, where USU plays, are just as loud but USU has a lot more students that are at the games. Having said that, the Spectrum is not Cameron Indoor Stadium, where Duke plays. Cameron is most definitely sacred basketball ground.


The quote for this week comes from Neal A. Maxwell

‘We can learn that at the center of our agency is our freedom to form a healthy attitude toward whatever circumstances we are placed in!’

Second Semester

Yay, a new post! Sorry about not posting anything for a while. The end of the semester/Christmas/beginning of the semester kind of threw me off. All I have to say about my long winter break is that I am glad it is over and I’m back in school. I love to be busy, especially busy with biochemistry!


This semester I am taking two classes and a few seminars (I am sitting in on a class trying to learn Java too). The two classes that I am taking are physical biochemistry and a structural biochemistry course. The two seminars I am taking are the Biochemistry (departmental) seminar and SBB (Structural Biochemistry and Biophysics). Speaking of SBB, I have decided to affiliate with SBB since my dissertation research will likely be in, well, structural biology and biophysics! All this really means is that the Department of Biochemistry will award me my degree and I will get a certificate from SBB.


Also, I am currently in my third and final (thank goodness) rotation. In the beginning of March I will have to choose a lab that I want to join. The rotation that I am in now does NMR (Nuclear Magnetic Resonance) of macromolecules (big molecules or proteins to the layperson). In there I am learning magic (a.k.a linear algebra and complex math; i.e. imaginary numbers) so I can do some computer programming for the lab. All I can say is math is SO COOL! Without math we would all still be naked, running around Africa (When watching the monkeys in Washington DC, seems like we’d be better off naked in Africa).


The weather here has been erratic. In January, we were enjoying sunshine and 60s. However, the last two weeks have been cold and rainy/slushy and even snowy (albeit, nothing like what my brother, Shane, has got up in northern VA).
Mostly it has been cold and rainy; cold enough it should be snowing but its not.


Its entirely to late so I shell leave you with my ‘quote of the post:’


“It requires a very unusual mind to undertake the analysis of the obvious.“
Alfred North Whitehead (1861-1947) English philosopher and mathematician.

Thanksgiving

I am now done with all my classes so I can write a post about Thanksgiving break. I didn’t know what I was going to do for the break until about a week before. Shane and his family decided to stay home for Thanksgiving rather than head up to Maine. So, I decided to head up to northern Virginia. However, I had a very difficult time trying to find a ride up there; I had already secured a ride home with someone in my ward. I have an awesome roommate who sent out a massive email trying to find someone going up to DC and she got a bite, I got a ride! Just like a miracle! :)

It was a GREAT Thanksgiving break! I wet up there on the Tuesday before Thanksgiving and stayed until Sunday. I spent a little time on a final paper but it was mostly a very relaxing weekend. We mostly hung out on Tuesday and Wednesday doing whatever; watching movies, playing video games, sword fighting (contact me for further details), etc. Thanksgiving was good; we had about 25 people there. Tyler Moselle and his girlfriend came, it was great to see Tyler again and to meet hi girlfriend! They are great! Other than that, the rest of the people were families from the ward and the sister missionaries. We had lots of yummy food; turkey, stuffing, cranberries, mashed potatoes and gravy, rolls, pie, etc. It was a fabulous dinner! We then went to see 'The Blind Side.' AWESOME movie; I highly recommend it!

Friday was really fun; we went to a Christmas tree farm. It is right by Shane’s house so the drive wasn’t like the drive’s we took to get Christmas trees in Utah. Luckily, Katie took a lot of pictures; so I’ll tell the story with the pictures.

The Christmas tree farm was up on a hill. This is looking out, off the hill.

The Family

Which tree...?

Mike cut the tree down.

We took turns pulling the tree.

The employees than put the tree on a big shaker to get rid of dead needles.

They then wrapped the tree up.
It was a great day!

We then went home and put the tree up and decorated it.

That was pretty much the weekend. Great time with great people!

Walkingg to My Lab

This morning I had a very interesting walk to my lab. As I was about to descend some stairs, I noticed two policemen interrogating a guy on a park bench. As I got closer to the scene, it became rather obvious that the man had decided to stay the night on the bench. From the looks of it, he had a very late night of drinking and had not yet slept off the affects of the alcohol. I had to chuckle as I walked by and heard him struggling to answer the officers' questions. I must stress that this is very atypical of Duke. Or perhaps it isn't and the good officers just had a late morning. :) Either way, it added quality entertainment to a rather mundane walk across campus.

Second Rotation

I attempted to upload a picture but couldn't...sorry :(

I have finally started my second rotation. I was supposed to start it about two weeks ago but I had to wait for my post-doc mentor to finish up his dissertation. I didn’t mind the time off as I had most my time occupied with plenty of class related activities. The rest of my time was filled with writing three essays for an NSF (National Science Foundation) fellowship application. This NSF fellowship is kind of a big deal; in all I’d be getting a tad over $120,000 over three years (not all at once and not directly to me). In my second rotation I am trying to redesign a protein so that it will bind a new molecule. So currently I am spending a lot of time looking at this protein to possibly add a modification that will allow the protein to bind the new molecule. Ok, enough science.


I went to my first Duke Basketball game. Even though it was an exhibition game, the arena was full. It will be fun for the season to begin! Duke Football is currently on a three game winning streak and have an ocerall record of 5-3. The new coach is doing AWESOME in his second year! Keep your eye on Bluedevil football; they may surprise you.


I have found that I am horrible with names, which I kind of already knew. It is extra pronounced in my church. Unlike Utah, here I only see the people in my ward for a few hours on Sunday. It has been quite embarrassing to forget someone’s name when you know you’ve asked them twice already. I am learning name slowly. The ward here is awesome! An interesting fact: most of the grad students in the ward went to undergrad either at BYU or USU. I have yet to meet an Utah alum. ‘


There you have it; my life, in order from Monday to Sunday; school, sports, and church.