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.

Bear Lake & Dystonia

Last Wednesday I went up to Bear Lake again, this time with my family. We stayed until Saturday, My parents, Grandma Jensen, Becky’s family and Jonna’s family were all there. We stayed in a condo on the west side of the lake, Unfortunately, this has been an unseasonably wet June and it rained everyday except Friday. Friday was a beautiful mostly sunny day but it was too chilly to have an enjoyable day on the beach. Luckily there was an indoor pool where we spent a lot of time. The kids had a blast swimming; even the two babies (Kenedie and McKinley) enjoyed it!

Random tidbit: I have started ‘The Fellowship of the Ring…again. This time, though, I really believe that I will finish it.

I have to share a link that was sent to me about dystonia:

Tyler's Hope

This family is dealing with primary dystonia; I was diagnosed with secondary dystonia. I have contacted the father, Rick, about helping the Tyler’s Hope organization. He replied and expressed interest in having me be a science advisor for Tyler’s Hope, as well as promoting the organization. If you have a desire to give money to someone other than the IRS Tyler’s Hope is an excellent option. 100% of funds raised goes to research! Visit: www.tylershope.org