Edgar Meyer, Double Bass

This evening I went to an amazing performance by a very talented artist, Edgar Meyer. Meyer plays the double bass, the largest and lowest-pitched bowed string instrument in the modern symphony orchestra according to Wikipedia. He first played Bach, Suite No. 7 BMV 1007 to be specific. Then he favored us with some of his own work  and work of other modern composers. Overall the performance was outstanding; Meyer is truly a master player. The pieces selected were varied, which I appreciated. Bach was Bach, I enjoy Bach a great deal but it was something I've heard before. The rest of the pieces were new and I really enjoyed them. The two that I thought were most excellent were 'Barnyard Disturbance' and 'Pickles' (which was entirely strumming). Here is a piece for your hearing pleasure.

Barnyard Disturbance (try to imagine just the bass solo)

It was a great performance!

Duke UNC round one 2012

Earlier this week I found out that the first Duke vs. UNC game of the season was coming up. I had no idea where I was going to watch the game. Last season I watched it with my lab mate, Daniel; we lost that game. As such, I decided it would be best if I find another venue, because where I watch it definitely determines the outcome of the game. The LDS institute was showing the game and my roommates wanted to go. I was hesitant at first as the institute is in Chapel Hill near the arena where the game was taking place. Plus most of the people who hang out at the LDS institute are UNC students. Was this really a good idea? In the end I decided to go.

The first half was pretty tight, I’m not sure how tight as I was actually working on lab stuff the whole time. The second half was disappointing, that was until the final two and a half minutes. Harrison Barns made a field goal with 2:38 left putting the Heels up ten. Then the Blue Devils went on a run, complete with Tyler Zeller (UNC star) tipping a three point shot in for Duke, but it was a two since it was tipped in, by a Heel mind you. With 15 seconds left, and no timeouts, Zeller made a free throw putting the heels up by 2. What happened next makes this game an instant classic. The Devils whittled away the clock not wanting to give the Heels time at the other end. With mere seconds left the ball was in the hands of the most productive player on the court, Austin Rivers (yes, Doc Rivers son). At this point in the game Rivers had 26 points, 15 of which were 3-pointers, he was 5-9 from behind the arc. So with the game on the line the ball naturally goes to him. Despite the fact that he had demonstrated incredible proficiency from deep Zeller, the 7-footer who was guarding him, decide, ‘Hey, its Austin Rivers, I better give him plenty of room!’ Rivers shot, the buzzer went off, and then the Tarheels hearts were ripped out as the ball hits the bottom of the net. The four Dukies in the institute, myself included, went wild as the other 25 Tarheels were attempting to process what just happened. It was unbelievable!

As I drove back to Durham with my two roommates, Han and Mat, we decide to go on campus. We went to Cameron where the team would be arriving shortly. There was a fair amount of students and avid fans awaiting the arrival of the team bus. There were intermittent chants reflecting the excitement ignited by a magical finish. For fifteen minutes the crowd grows and then the bus finally arrives. The bus can’t get near Cameron due to the crowd so they let the players and coaches out 30 yards from the arena. The players were having a good time with their fans as they headed toward Cameron. Just to give you an idea on just how crowded it was, at one time I was in the middle of a tight pack group; I was probably touching 5-8 simultaneously. The crowd was so tight that it moved as one entity as the players pushed there way through. At one point I was right next to Austin Rivers as he got up on a small ledge letting out the excitement, which I’m sure was fed straight from the crazy fans.

This was a night I will not forget!

Post Prelim

I was a cowboy for Halloween!

This has been a great week. The week started on Halloween when I had my preliminary exam. This is where I gave a thirty-minute presentation on my dissertation research proposal and then get questioned about my proposal and general biochemistry. As it turned out I was asked next to nothing about general biochemistry, I guess my proposed research was just that interesting. The research topic is rather unorthodox within the realm of scientific research. Almost all scientific research is hypothesis based; one proposes a hypothesis to explain an observation and then goes about to find supporting evidence, or lack thereof, of the said hypothesis. In contrast, my research is exploratory in nature. What this means is that I have no hypothesis, I have to go out and find one first. This fact led to a lot of interesting discussion in the prelim, which kept all of the questions on the research. The exam went a lot quicker than I was expecting. I passed and a celebration ensued. After the canonical lab party, the celebration continued as my lab mates and roommates took me out to Bull City Burgers. It was great! 

On Tuesday I didn’t even go into lab, I needed a break after a solid month of studying for my prelim. Instead I helped out the missionaries; first, by taking one to a transfer meeting and then bringing a new one back and, second, by taking them out to dinner and accompanying them to an appointment. The rest of the week was spent either in the lab or in the yard. I got back to lab quickly, researching the usefulness of map correlation coefficients. Since I let the yard go while I was preparing for my prelim it was in desperate need of TLC. I cleaned up fallen branches, raked leaves and weeds, mowed the lawn, turned the soil over in the garden, etc. There is still plenty to do. 

On Friday night I went to a concert given by Ingrid Fliter, an amazing classical pianist. I am absolutely in love with piano music. She played Beethoven and Chopin. It was nothing short of incredible! The pieces that she preformed were rather fast paced, thus her fingers were moving at a hundred miles per second up and down the keyboard. She made it look easy. Saturday I went to the volleyball game which is always fun. 

Looking forward, I have to get ready for a talk that I have to give at department retreat, which takes place this weekend out on the coast. I will then focus 100% on my research.

Fish

One of the coolest textbook figures I have ever seen! YAY randomness!!

"Principles of Biochemistry,"  Fifth edition by Moran, Horton, Scrimgeour, Perry.  Pearson, Boston: 2012. page 278

The preliminary exam prep

Well, it has been quite a while since I have written now, has it not? A lot of rather neat things have happened since my last post. As you know I am getting ready for my prelim, the exam I need to pass to officially become a PhD candidate. ‘Prelim’ is short for preliminary exam. OK, what’s that?

The preliminary exam consists of two major components, the written and the oral. By far, the oral is the bigger part. Don’t get me wrong though, the written is pretty tough too. The written is basically an NIH grant proposal where the student proposes what they will do for their dissertation research. When doing a dissertation a committee has the job of judging the research, make sure that the student is really doing PhD level work. When you hear a PhD candidate say that they are going to defend, it is the committee to whom they defend, they are defending their dissertation research. But that is still many years off for me. Back to the prelim. I have completed the written portion of the prelim (research proposal). The committee then inspects it and, if needed, requests revisions. I am at the point now where I have received the revision requests and am making those. I should be done tomorrow, at which point I will send a final draft to my committee. The oral takes place in two weeks.

In the oral the student, me, gives a 30-minute presentation on the proposed research. After this the committee asks questions to the student pertaining to not only the proposed research but also any topic in biochemistry. The questioning usually lasts for 2+ hours. Based upon your answers the committee will either pass you, thereby declaring the student competent to pursue the proposed dissertation research, or fail you. If the student passes there is great rejoicing. If they fail the student hits the books harder and then tries the prelim again in a couple months. If the student fails twice Duke will hand out a Master’s degree and send them on packing. “Thanks for trying!”

Random Crystal

So there you have it. I am right in the middle of preparing for my orals, studying my butt off. The main problem with my research is that it is more physics than biochemistry; remember that the committee can ask any question pertaining to the field of biochemistry. So basically I am trying to relearn material that I learned 4 years ago at Utah State. I rarely feel stressed, its just who I am, almost nothing in this world is so serious as to cause stress, right? However, this past week I have felt pangs of stress as I have come to realize that I don’t, and can’t, know everything that I think I’ll need to know for the prelim. I have received a small amount of comfort as I was told that, in the end, the committee is more concerned on how you can reason rather than how much you know. Still, the best way to prepare to reason through biochemical problems is to study biochemistry and gain as much knowledge as is possible.

With two weeks to go I feel there is a long way to go before I can confidently declare that I am ready.  Nonetheless, I feel like everything will work out just fine.

SBB Seminar

This past week has been rather busy for me but also very exciting. Busy because I had to give the seminar talk in front of my whole program on Monday. That includes graduate students as well as faculty. Further, the seminar talks are usually 50+ minutes long; I had never given a presentation that long before. The problem was that although I have done a lot while I've been here, the stuff I have done isn't very presentable. I needed a concrete example of the use of a method for which I had made tools for. Its like I had made a sledge hammer, something brand new and never before seen, but I had yet to show it could tear down walls. Thus, the last week or so was not filled with antagonizing over what to say or how to present my work, rather it was doing the work so that I had something to show for it. Now I will explain what I actually did, so feel free to skip the next paragraph.

I work on methodologies to improve model accuracy given low-resolution crystallographic data. I am specifically focusing on proteins. Getting an accurate model with little error at low resolution is very difficult. In fact, there has yet to exist a mode with little error given low-resolution data. In order to get an accurate model one needs to have a good backbone. This is like saying, in order to have a sound building you must have a solid foundation. Current low-resolution structures don't even have good backbone. There are methods by which you can use hydrogen bond restraints that will keep certain regions of the backbone look like they are suppose to look. These are like extra support for the backbone. However, defining these restraints is fairly tedious. In fact, this process is simply not tractable for large molecules. My tool allows one to easily defining hydrogen bond restraints. After you do this you have to put your model through a process called refinement, luckily the computer does this step. The is where you can get backbone errors but hopefully the restraints keep the errors from occurring. So what I did was take a low-resolution model and refined it without and with several different restraints. The results were good, kind of. The backbone in regions where hydrogen bond restraints were defined looked great. However, other areas gained more errors. That means more research for me, YIPEEE!

Suffice it to say that the presentation went better than expected. I had practiced the talk the day before and got worried because I quickly got tired and my dysdtonic movements got worse making it even more difficult to talk. All though this worried me I was relatively calm going into the seminar. I decided to do something unorthodox that I had done before which is to sit rather than stand to give my presentation. It worked like a charm. I also believe that I did better live because I was getting feedback from the audience. I made them laugh, I could tell that at least some in the audience were engaged, and asking rhetorical question at the right time to further engage them. It was great. I got two similar comments, that I've actually received before, saying that my use of humor was great and actually added to the presentation. I am glad it is done now though!!

Now onto the exciting news. Las fall I had applied for two fellowships. One through the NSF and the other through the NIH. These fellowships pay for my stipend and one helps with tuition. This simply takes the burden off my PIs. I heard back from the NSF and I got the fellowship! After I had received the award letter I decided to check the status of my NIH fellowship... The status bar said that my application had been reviewed but I would nor receive word on wether or not I got funded til council meets in May. However, I was able to see the reviewers comments and the score that the gave me. The score I go was 10. OK...what does that mean? When I started reading the reviewers comments I knew 10 had to be good as there were very little criticisms. But I didn't learn what 10 meant, I went to the web for that. It turns out that what the reviewers do is score the application on different criteria on a 1-9 scale, 1 being the best. then all the reviewers come together, average their individual scores and time by ten to give you your overall score. That mens that the overall score ranges from 10-90. I was flabbergasted! Now I have to see if they'll fund me. I think they will. Now I have to see if I can take both or choose one. This is a dilemma that I don't mind having.

NIH Grant, DONE!!!

Sorry I haven’t posted for a while. Suffice it to say that I was preoccupied; I was writing a ‘big’ grant for an NIH fellowship. Big relative to this stage in my ‘career,’ if you will; I’ll be writing much bigger grants in the future. It was due yesterday and I was able to get it in with a whole 11 minutes to spare! The final product was a 42 page PDF! Luckily I did not do it on my own. I have to thank Dave and Jane, my PIs, Marsha Brooks, our staff assistant, and my three referees (those who wrote reference letters; Sean, Joanie, and Terry). Now I can get back to doing graduate stuff, a.k.a research. I am excited to get back into the research, It’s difficult but the challenge comes with numerous learning opportunities. It is my personal belief that learning, personal growth, and happiness are synonymous.

For Thanksgiving, I went to NOVA (a.k.a. northern Virginia) where my brother’s (Shane’s) family were kind enough to host me. It was a great dinner but the best part, as always, was to spend time with some family. I went up there the next week where I watched my Aggies play Georgetown, we didn't win but it was fun to see them play nonetheless.

I will work on my research for a week and a half and then I’ll be heading to NOVA yet again to spend Christmas with Shane’s family (thanks Shane). That is unless I find $600 dollars on my way to school, in that case I’d go back to Utah :).

Not much to this post because all my time has been spent on this grant. Until next time...

School Starts and Poison Ivy

Classes are about to begin here at Duke University, all this means for me is that I will start to attend seminars and begin my one-on-one tutorial on x-ray crystallography. I will be continuing my research that I was doing during the summer. My PIs returned from their summer at their cabin. I talked to both of them about what I was learning and proposed I side project. They were both enthused about what I was already doing and what I had proposed. I will, as always, be busy; I’ll never have to say ‘I wonder what I will do tomorrow?’

I had my first exposure to poison ivy and can say I react very badly to it. I went to the doctor and she prescribed some medicated cream and Benadryl. However, the thing that I think worked the best was a $16 4 ounce tube of poison ivy scrub. It took about two weeks in all to get over it. The only place I can think of that I contacted poison ivy is when I was weeding in my back yard. However, subsequent investigations of the yard have yet to identify any poison ivy. I am a little more tentative about working back there now. Enjoy the pictures below.

The quote for this post comes from last General Conference in which President Uchtdorf gave a great talk on patience in the priesthood seesion:

‘There is an important concept here: patience is not passive resignation, nor is it failing to act because of our fears. Patience means active waiting and enduring. It means staying with something and doing all that we can—working, hoping, and exercising faith; bearing hardship with fortitude, even when the desires of our hearts are delayed. Patience is not simply enduring; it is enduring well!

Ashley''s Visit

Sunday July 18, 2010

Last weekend my niece, Ashley, came to visit from northern Virginia. We had fun just passing the time with each other. We toured Duke campus and went to see Toy Story 3 on Saturday. Of course, the Duke campus was magnificent, you kind of get use to it when you se it everyday so it is a treat to show someone else around. Toy Story was also magnificent and I HIGHLY recommend it. That night we went into my lab and played Wii Fit Plus. Our favorite game was an obstacle course that you had to run/jump through. On Sunday we went to church, took it easy, then we watched a movie. Monday we went to Eno River State Park and out to lunch. Due to unforeseen circumstances, I decided to escort Ashley back to northern Virginia as well as take my roommate to DC. I then left the next day, a quick trip but well worth it!

The rest of the week was spent designing a poster for a conference that I am attending I Chicago. The conference is with the American Crystallography Association and I leave this coming Saturday. The poster is coming along but is most definitely a work in progress. I hope to finish it up by Wednesday so I can get it into the printing company. I am in Chicago for 5 days then I go to Utah! I’ll be in Utah from July 29-August 9.

Here are some pictures from Ashley’s camera:

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.

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.

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!

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