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.

Hi folks! Bradley here (yes, Bradley is my name not Brad; see my birth certificate for further details) reporting on the goings on in his life.

Last week marked the official date that my second rotation was to begin. Despite this fact I spent all of last week in the Richardson lab (where I did my first rotation). I have a second rotation lab just no project. I did not mind this because I am super busy with classes. In two of my classes I am reading two papers for each class a day and in another class one paper a day. That comes out to be 12 papers a week. These are scientific articles so you can't just quickly read the paper and expect to understand them. You have to really pay attention to what you are reading. So it takes a lot of time.

I went to a Duke Basketball team scrimmage which was a prep rally too. it was really fun. Even though I had been inside Cameron Indoor Stadium, quite a historic venue, I never realized how small it was.

Anyway, that is all I have unless you want to read about the molecular mechanism behind allostery. The Aggies did win their second game of the season, way to go! I would like to thank TCU, they did a great job destroying, dismantling, and otherwise embarrassing BYU. I only wish the slaughter would have been on TV (stupid Mountain West Conference, grrr!!)

Last week The Richardson lab moved into a new space. Since the space is so radical I have decided to share a few pictures. Here they are:My work station.

Conference

So this weekend I went to visit Shane's (my bro) and his Family. I got a ride up to Washington with other students that also go to Duke and Shane picked me up on the Mall. We had a lazy weekend sitting around the house, just what I wanted.

Saturday we went to watch my nephew's, Mike's, football game. Mike was injured and couldn't play. The Tuesday before Mike's jaw had a tragic collision with his Brother's, Nick's, knee during a front yard football scrimmage. He had to have surgery to fix two fractures. His jaw is wired shut for a month and he has to have nothing but liquids for six weeks. It's tough but he's a trooper.

We then went to the Priesthood session of General Conference. It was an awesome session with great talks. I love that the Lord has provided a way for us to learn and grow. It makes me so happy!

Sunday we watched conference while Becky was so kind to give everyone a foot massage with her oils. Thanks Becky, it felt great! Sadly I had to go home Sunday evening despite the fact that I have fall break and, therefore, have no class Monday of Tuesday. The bright side is that I can get my homework done!

I hope all of you are doing great. Drop me a line and let me know.

Duke Basketball Season Ticket Campout

So this last weekend I attended the well established tradition of Duke Basketball Season Ticket Campout. For those who are not acquainted, allow me to give background info. Basketball at Duke is s HUGE deal. Duke is consistently ranked in the top ten teams in the nation. The venue for home games is Cameron Indoor Stadium. It holds less than 10,000 spectators. It is, arguably, the toughest place for an opposing team to get a win. The student spectators are affectionately referred to as the ‘Cameron Crazies.’ As you can imagine, acquiring tickets at such a venue is not an easy task.

Duke, like other schools with great basketball traditions, has a lottery system to attain tickets for their graduate and professional students. This was implemented in attempts to make it fair, but not easy, to get tickets. Unlike other schools you have to endure a 36 hour campout to even get your name in the lottery! This is known as the Duke Basketball Season Ticket Campout.

A few weeks before the campout, everyone who wants to participate must register online. The campout starts at 7PM Friday and ends at 7AM Sunday. We were allowed to set up our tents Thursday afternoon. We had to check in by 7PM Friday. We claimed a spot Thursday by setting up our tents. That was the easy part. Getting to our spot Friday was fairly difficult. Some people opted to bring U-Hauls to sleep in rather than tents. Now how many people are we talking? Well over 2,000! Traffic was a nightmare, U-Hauls everywhere, we weren’t allowed to unload anywhere near the site, and it was hot and humid. We had a lot of food and two coolers; one of which could easily be used to hide a body (that had all the beer). We had to haul those for about a mile.

Once we were settled we checked in and they explained how the campout worked. We were not to leave and to ensure that we didn’t they held roll call at very random times; we had no idea when it was going to happen. The way it worked is a siren would go off and then everyone, a 2,000 plus, had to join their line, designated by last name. They were about 15 different lines. They then checked your name off surprisingly fast. If you had not checked in within ten minutes of the siren going off you had officially missed the check in.

The first check in was not until about 11PM. Then there were a few more until after 2AM. The check ins started up before 6AM and were very random throughout the day. They again did check ins until after 2AM Sunday morning. They then called us at 5AM and told us to begin the end of the campout. They had us clean up EVERYTHING before they would let us know the results of the lottery. We had to take all our gear to our cars. We also had to have all trash put in the dumpster. We were not done until 8 at which point we got into our lines. We went up individually and were told if our names were put in the lottery and if we were selected to buy tickets.

So there is how the lottery went. The rest of it was a HUGE 36 hour party. Complete with copious amounts of alcohol and loud music. There was very little sleeping. The girl’s basketball team came to visit the first night. We all went to listen to them. The second night was a real treat. The men’s basketball team came, even Coach Mike Krzyzewski (Coach K)! He is a legend! He currently is the head coach of the USA Olympic Basketball Team. He, along with his team, won Gold in Beijing in 2008. He explained some changes at Cameron and how we should act as fans (be loud and irritate the opponent). He then took questions. Let me say I’m glad I didn’t ask him a stupid question; he doesn’t like those! Suffice it to say he came across as very arrogant and surprisingly rude. The arrogance I don’t mind, he has accomplished a lot (not that that’s an excuse). But the rudeness I could go without.

To wrap it up I won tickets! We had a group of five, three of us won tickets (we beat the odds; there were only 700 tickets). We will divvy up the ticket and the cost thereof between the five of us.

There you have it. It is now entirely too late. I will say Good Night! GO BLUEDEVILS!!

Here are some pictures.

My Homework

I thought I'd share my PhD level homework. We were given a coloring book and told to color two figures. Who knew Crayons would be required for graduate school? Thank goodness for Photoshop!!!!!!!!!

Can you see the 3D character given my shading?

PhD programs are tough!

Two Weeks!

Random Picture: Wellsville Mountains 2006

I have, thus far, been in class for two weeks. I am taking three seminars and two lecture/discussion type classes. We do a lot of reading! We read articles out of scientific journals and then have group discussions. There are no tests. Interesting; but why?

The idea behind this is that we are being trained as scientist, research scientists to be specific. As undergraduates we were taught principles of various aspects of science and then were tested to see if we had learned the principles. This approach does not allow too much wiggle room to seriously question what is being taught. Sure, as undergraduates we can ask, ‘how do they know that?’ If known, the professor can explain an experiment that was used (or may have been used) to ascertain the information. In undergraduate courses this system works great because the courses, for the most part, teach established data. However, as “PhD’s in training” we are now focusing on how scientific knowledge is gained. Also, if we are given a lecture, the material will most likely be penetrating the current boundaries of knowledge. It does no good to read an article and then say, ‘That’s it; we’ve figured it out.’ We need to seriously analyze the data and see if it makes sense. As scientists we have the responsibility to question the publication and, if we have the same research emphasis of the article’s authors, perhaps perform experiments to confirm or discredit the publication. Enough on the processes of scientific discovery.

This last week I started my first rotation. Again, a rotation is an eight week projects in a research lab that allows the student to essentially ‘test drive’ the lab. We do rotations in three different labs and then we can choose the lab that fits us the best. There is a story about how I got into my first rotation. I was looking at three different labs for possible rotations. There was a fourth lab that actually really wanted me. They had a computational project and I was an obvious fit as computation is all I do. However, working at McDonald’s was slightly more appealing than working in that lab.

Anyway, I had three labs that I was seriously considering for a first rotation but none of them could really take a student for the first rotation. Two were going to be gone for most of the first rotation and one was moving to a new lab. So I had a choice; see if I could rotate with the lab that was going to move or I could go to the fourth lab that really wanted me. I took the former course of action. When I explained the situation the PI, he said that I could do a rotation despite the eminent move. Now they have another set of hands to help move!

If you care to know what I do in my rotation, by all means keep reading. If not, that’s perfectly fine; I’ll say good bye and thanks for reading.

In my rotation I am working with a husband and wife team; the Richardson’s. They are very significant figures in the field of computational structural biology. In the lab I am trying to find patterns of errors in low resolution models. Now what does that mean?

(Disclaimer: The following may not be scientifically correct but gets the correct ‘concepts’ across nonetheless.) Protein structures (models) are made from shooting a crystal of the protein with x-rays. For the current discussion suffice it to say that we take very crude ‘pictures’ of the protein (scientists: please read disclaimer). Imagine a picture of a clock. At high resolution we can see the hands, the numbers, the screw holding the hands on, flaws on the face, every little detail. With this ‘picture’ we can then make a fairly accurate model of the clock. But you very well could have a low resolution ‘picture’ too. You can imagine that it is going to be difficult to make a model from this ‘picture.’ However, when low resolution is all you have you do your best. My goal is to find patterns of errors in models derived from low resolution ‘pictures.’ I hope that made sense.

I hope you all are doing well. Feel free to drop me a line. Have a wonderful week!

The Difference Between USU and Duke

So this week was orientation week. We had the typical information sessions that accompany orientation. However, most of the time was taken up by PIs (Primary Investigators or research professors) trying to recruit us to their labs. As graduate students we have to do rotations. Rotations are 6-8 week projects that are completed in a research lab. We have to choose three labs that interest us. After we complete the rotations we then choose one of the three labs to do our dissertation work (research) in.

I have one lab that I will definitely do a rotation in, the Richardson Lab. There is another lab, the Oas Lab, that I may rotate in. The PI of this lab is trying hard to recruit me. If I were to join this lab I would be here a long time as I would be required to take upper division stats and math (differential equations and linear algebra) before I could really dive into the research. I have yet to choose a third lab to rotate in.

The week is not done yet though. Tomorrow we set out for Beaufort, NC where we will receive ethics training. We will be taking buses and will stay til Sunday. Beaufort is on the coast; we get to play on the beach.

One day this week was the Graduate School orientation. This was given by the Duke Graduate School given to all new graduate students rather than the small department orientation. There were quite a few speakers and a question and answer session. One thing that hit me was something the provost said. Duke is such a great university not because they’ve somehow magically arrived at some whimsical state of being rather they recognize that such a state is false and improvement is constant. They are constantly looking and implementing improvements. I really liked that.

There was a faculty panel that then took questions. Before that though, they each said a few words. I was able to relate to what one of the faculty members said. It reminded me of a lecture I received fourteen years ago as I left elementary school and was about to enter middle school. One of my sixth grade teachers told us that although, as sixth graders, we were the fearless leaders that the younger kids in the elementary looked up to, things were about to change. She said that as seventh graders we were going to be relatively irrelevant. I believe her exact words were that we were going to be ‘just another fish in the pond.’

Anyway, back to present day Duke. One of the professors told us that we had gotten into Duke, something that, she assumed, we bragged to our friends about. Indeed, this was no small feat. The Duke Graduate School received over 7,600 applications but there were only 689 new students. Then she put us in our places by saying that we may have been stars at our undergraduate schools but here the playing field had been leveled. I find this to be very true for me.

At USU I was a star receiving many different accolades. I was even recognized university wide by receiving the Legacy of Utah State Award. In Utah I would tell people that I was pursuing a PhD in Biochemistry and most were amazed at both the degree and field of study. Here at duke I am indeed just another fish in the pond. No one is impressed that I am getting my PhD, but that is because they are also pursuing the same degree. I can actually talk about my research and the listeners actually know what I am talking about.

Having said that; I know that I am here to be an example beyond academia. I know to be that example I just need to do what I do. Which, ironically, is do what all my peers are doing; pursue my degree.

My home in Durham!

My house as you walk in the front door.

My Room as you walk in.

The house

Looking down one direction of the street

Looking down the other direction of the street

The Back Yard

The Move to Duke!

Here I am in Durham, NC. I have moved into my house where I am currently living with Jeremy, who owns the house, and two girls that are summer interns. The girls are moving out this weekend. I will be getting three new roommates by the time fall semester starts; two girls and a boy. Of course, Jeremy will still be here. Stay tuned for a post with pictures of my new place.

Here I am starting out in Logan, UT.

The drive was long but fun. I got to see a lot of places that I had not seen before. I loaded my stuff in Logan then my friend, Clark, and I drove to St. George where we loaded Dallin (Clark’s brother) who will be attending the University of Georgia. We stayed the night there. The next day we headed to Albuquerque, NM. I drove the U-haul from Marble Canyon to Flagstaff.

Here I am ‘standing on a corner in Winslow Arizona.’ Probably the ‘dump’ city of Arizona.

The next day we went to Oklahoma City. Not much to tell about this day. It changed from desert to grass lands. I drove the U-haul the length of northern Texas.

The next morning we went to the Oklahoma City Memorial. It was a very sacred place; very beautiful.

Here is the reflecting pool.

Here are 168 chairs to honor each victim of the tragic event.

We then drove to Memphis, TN. This is where we started to see the trees. In Memphis we went downtown. It was Saturday night so they had the streets blocked off. There were tons of people! We tried to eat at the Hard Rock Café but there was so many people we couldn’t be seated. We ended up eating al Wendy’s.

Here I am in Front of The Hard Rock Café in Memphis.

The next day we drove to Athens, GA. This drive was pretty much solid trees. We stayed the night in Athens and in the morning we moved Dallin into his new apartment. Clark and I the drove to Durham, NC. After we moves my stuff in we returned the U-haul.

Here I am at Duke!! YAY!

There you have my road trip in a nutshell.

Bells Canyon Backpacking Trip

I have been very busy getting ready to move to NC an wrapping up things in my lab. Besides that I have no excuse for not posting anything. :) I start the long drive this Wednesday!

I have been at my parent’s for the past couple weeks and have been doing a lot of hiking. This past Monday I started a backpacking trip up Bells Canyon here in Utah. Bells Canyon is probably the most beautiful canyon along the Wasatch, but I am not biased at all:). There is abundant amount of water year round. There are even bogs up there. It is so green that those not acquainted with the Wasatch would hardly believe that they were in Utah.

I went up with three young friends; Christopher Davis, Austin Duncan, and Bryan Miners. We started hiking at 6 AM Monday morning. We had packs ranging from 35 to 45 lbs. The trail is said to be 4 miles (it feels longer though). There is a 4400 foot elevation gain; so the trail is rather steep. We made great time; we were at Upper Bells Reservoir (were we camped) just after 11 AM. We spent three days swimming, hiking, and just goofing off. We came back Thursday. Here are some pictures from the trip.

Upper Bells Fall

This is a meadow above the Upper Reservoir

This is The same meadow as above

This is a stream in the meadow

This is looking down on the Upper Bells Reservoir

Me in a meadow further up from the first meadow

Christopher In the upper meadow

A stream near the upper meadow

A stream near the upper meadow

The upper meadow

Decending from the upper meadow

This was a solo hike I did (the boys were pansies and didn't want to climb the extra 1,750 vertical feet to the top). This is on top of South Thunder Mountain.

Looking at the back side of Lone Peak from South Thunder Mountain.

Looking south from South Thunder Mountain. Box Elder peak is in the foreground and Mount Timpanogos is in the background.