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

Gratitude

During a church service I received the distinct impression that I should be more grateful. As such, I dedicated myself to write down something that I was grateful for each day for seven days. This is what I came up with.

Sunday, October 16, 2011

I am grateful for my intellect. The ability to learn and grow is the very essence of true happiness. We must learn how to love, how to behave, how to serve, how to relate; we must even learn how to learn. Learning is something that we will do as a consequence of being conscientious. The choice is ours as to what we will learn. As a garden, it takes a great deal of work before something beautiful emerges but even left unchecked something will grow. It is therefore up to us to decide what we want to be. If we desire to be great we must begin by learning the attributes of greatness and then learning how to personally gain those attributes.

Monday, October 17, 2011

I am grateful for friends. Friends are truly God’s gift to His children. While I associate with many people at school and church, great friends occupy a much smaller circle. They are those who I know genuinely care for me; they even care for my silly pursuits simply because they are my pursuits. Friends are those who ask, ‘How are you?’ and sincerely mean it. While we may have true friends that sincerely care for us, it is us who chooses to let those people into the intimate aspects of our lives. If we do so we can find greater happiness than we can ever experience alone. The power of kindness, caring, and genuine love that true friends provide is yet another manifestation of our Father’s love for us.


Tuesday, October 18, 2011

I am grateful for my body. I have been given a great body that can do a myriad of awesome tasks. Sure, it doesn’t work as most bodies work. Fine motor coordination? Shot. Balance? Not so great. Voluntary muscle contraction? Yes, at least for almost all my muscles I control them. Look at what else I can do. I can ride my bike for several miles, I can hike, I can sleep and eat. If you really think about it, I can move the way that I want to move pretty much unimpeded. I can also think, learn, solve complex problems, perform dissertation research in biochemistry. Cycling, hiking, learning, growing...are these not synonymous to being happy. It is true, I am very grateful for my body.

Wednesday, October 19, 2011

I am grateful for my two wonderful PIs (primary investigators), Dave and Jane Richardson. They are my mentors here at Duke. I am especially grateful for their enthusiasm for science; it makes research in their lab exciting. They are extremely supportive of their students; they both are helping me a great deal to prepare for my prelim. I literally can think of no other scientists that I would rather work under as a graduate student than Dave and Jane. The research that is done in the Richardson lab is not only extremely interesting but also rather unique. They are both great scientists and I feel privileged that I get to benefit from their mentorship.


Thursday, October 20, 2011

I am grateful for hemoglobin. Yes, I just said that. I am studying allostery and as I am sure you all know that the prototypical model for allostery is the effectual binding of O2 to one of the subunits in the tetramer hemoglobin. I am now spinning on rollers rather than riding on the road. Stationary cycling allows me to focus on the aerobics side of cycling. I have been so grateful for all the hemoglobin in my blood willingly delivering the needed O2 from my lungs to my leg muscles as I stubbornly ignore their screams of ‘STOP!’, a.k.a. the buildup or lactic acid.

Friday, October 21, 2011

Today I am grateful for cold medicine, perhaps the only medicine that does what it is suppose to do. My body has been trying to come down with a head cold all week and finally succeeded today. Unfortunately, a cold seems to take the edge off my mental aptitude; as such, studying is useless. But hey, I have a presentation to get ready for! So I thank you Acetaminophen and Phenylephrine.


Saturday, October 22, 2011

Today I am grateful for computers. My fine motor coordination isn’t exactly what it could be. As such, I have a difficult time with many of man’s mundane tasks: drinking out of a glass, tying my shoes, buttoning buttons, and, of course, writing. It is glaringly obvious that the computer has helped out a great deal with my inability to write. However, my gratefulness extends much further than that. I love biochemistry; I better, after all I am getting a PhD in the subject. A short twenty years ago one would highly doubt that I, given my physical limitations, could even attempt a PhD in such a field. Almost all biochemical research was done on the bench, I guess that is still true. But here I am in 2011 with no doubt that I can get a PhD in biochemistry. For that I thank you computers!

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.

Utah State vs. Auburn

So you probably all are wondering how my ride went this weekend, right? As it turns out I got a call Wednesday night from a fellow Aggie here at Duke, Mitchell, who happened to have an extra ticket to the USU vs. Auburn game. When an opportunity like that comes along I take it!

I met up with Mitchell and two other Aggie fans, Eric and Eric, on Friday afternoon and we started the long drive to Auburn, Alabama. We went through South Carolina and Georgia before crossing over into Alabama. It was a long drive but the exceptional company made the trip go by quickly.

The next day we caught a shuttle to the stadium. Of course, there were a ton of Auburn fans tailgating around the Stadium.  This is where we first encountered the phenomenon known as Southern Hospitality. We were greeted more than several times with a “Welcome to Auburn” and a “Glad that you could make it down.” It made me ashamed of the way all the fans in Utah, choose any school you’d like, treat fans from other teams. I wish everyone could see what we saw and learn how you should treat others.

The game more than exceeded my expectations. Since we are Utah State and Auburn is the defending national champion I was only hoping that the Aggies would post a few points. I can honestly say that I have never seen Utah State play as well as they did that day. We consistently were getting first downs and marching right into the end zone. The Aggies had the lead most of the game. Unfortunately, USU’s weakness, the defense, showed as they let a ten point lead slip away in the final four minutes of the game. However, I was not disappointed! Utah State posted more yards than Auburn and the Aggie quarterback, true freshman Chuckie Keeton, looked sensational. I have little doubt about making it over 0.500 this year.

After the game we headed to Atlanta where we tried for an hour to get into the Boise State vs. UGA game but that didn’t work out. Sunday we went to the World of Coke in downtown Atlanta; it’s pretty much a Coke-a-cola museum on coke. The history of Coke with their classy marketing scheme was very neat. At the end there was a taste test where one could taste Coke products from around the word. Of course I didn’t taste any of it as my tummy cannot tolerate carbonation, but it was still fun to see all the different flavors of pop. After that we hit the road and made the uneventful trip back to Durham.

All and all it was a great time. Spending time with friends and making new acquaintances is always fun. I only hope that more road trips, with these great men, comes sooner rather than later.

Thank You!

I would like to take this opportunity to sincerely thank the many donors who have supported my ride to raise much-needed funds for the Easter Seals UCP of North Carolina and Virginia. Your generosity will help many children and adults with disabilities live a full and happy life. The ride was originally supposed to happen tomorrow and Sunday; however, hurricane Irene could not time her arrival at a worse possible time. It has started raining here in central NC this evening and will only get worse tomorrow. Thus the ride for tomorrow has been canceled; riding will happen only on Sunday. 

I don’t ride on Sunday and this Sunday is no exception. However, I will ride the 64 miles for the Easter Seals UCP! I plan on doing it next Saturday, weather permitting. There are a few details that I need to work out. An important detail is how I can pull off 64 miles without the support I was looking forward to. After the ride I will post the details on how it went.

Again, I thank you for the support. I never imagined that I’d be able to raise nearly $2000 in ten days. Your generosity is much appreciated. As a person with a disability I know how hard it can be to ask for help but at the same time that help is greatly needed. It makes it easier when people offer the help. You have assisted a great organization that specializes in offering needed help to those who may need it the most.

Thank you,

Bradley

Cycling for a cause!

As you are all well aware I love to road cycle. As of late I've been riding a lot; 25+ miles three times a week. I also love to help people by getting them to question their own perceived limitations. Last night I found an event that brings these two activities into one. This is a bike ride called 'Ride Without Limits' and takes place in Pittsboro, NC. This ride benefits the Easter Seals UCP North Carolina & Virginia (UCP is United Cerebral Palsy). As a rider I need to raise $250 to ride. BUT I am trying to raise as much money as I can for this great organization. All proceeds will go to help children and adults with disabilities, not just Cerebral Pal

sy. Here is a blurb from UCP:

UCP’s mission is to advance the independence, productivity and full citizenship of people with all types of disabilities, not just cerebral palsy. With a nationwide network of affiliates and help from people like you, UCP is making it happen. One legal battle at a time. One program at a time. One person at a time

I plan to do a 64 mile ride. However, I ride for a purpose!! I am asking that you give $1 (or $0.50, whatever fits your budget) for every mile but ANY amount will help! Please be generous and donate here:

CLICK HERE to Help Bradley Out!!!

Lets help people find the opportunities to live without limits.

Thank you,

Bradley

A Cyclist's Confession

My name is Bradley Joel Hintze and I am addicted to road cycling. It all started on September 9, 2006 when my friend, Bryan (a heavy bicycle user), invited me to volunteer at a feed station for a race known as LOTOJA, the longest single-day US cycling federation-sanctioned race. We were stationed a mile or so below the summit of one of the three mountain passes on the course. As we handed food and water bottles to the 1,000 cyclists (facilitating the addicts) I noticed a few tandems. I eagerly turned to Bryan and said, “We should do this next year on a tandem!” Bryan liked the idea and encouraged me further. I was innocently introduced to this behavior but you can see how quickly I was planning to use. A month later I spent a large sum of my savings on my own road bike.

The time spent cycling went down as the bitter Cache Valley winter settled in; however, I did relapse in the middle of the cold season. This is hard to relate but it goes to show how this addiction can screw up your thinking. It was in the deep winter, we had several days in which the temperature struggled to reach freezing. I remember the day well, it was a cold but clear and the roads were dry although snow did cover the ground that wasn’t road. I had had enough holding back and I went and I used my bike. The temperature on my bike computer read 30 degrees! Crazy.

Well the next summer I became a heavy user of bicycles with the help of Bryan. We rode all over town, sometimes on our own bikes other times on the tandem. I remember a few sessions of use that lasted several hours: Logan to Salt Lake, we rode around the Wellsville Mountains, Logan to Bear Lake THRU Idaho… you get the picture. These sessions gave me great highs but nothing can compare to the LOTOJA. A year after I had innocently volunteered at a feed station I was riding the race on a tandem!

The time between then and now is fuzzy at best. There was a time when I moved across the country and left my bike behind. I had eight glorious months where I was clean. Then spring came with its trigger for the addictive behavior, warm weather. I couldn’t take it; I needed to use. So I had my dad mail me my bike and started using quite a bit. It’s been a year and a few months since I’ve had my bike here in NC and it has only gotten worse. I am now a habitual user of bicycle, essentially no soberness. I use three times a week, mostly in the mornings before I start in lab.

So what are the effects? First financial, in order to be a serious user you need money. There is the obvious; you need a bike, not just any though, you need an expensive carbon-fiber frame with the fancy components. Then there is the attire that users adopt, spandex with special padding. I am talking cycling shorts and they are not cheap. Then there is the maintenance; a heavy user will, out of necessity, maintain their bike. This is not free either. Second, the time factor; using takes a lot of time. For recreational users a quick ride around the neighborhood will suffice. The hard user, like myself, will literally dedicate several hours a week using. Third, psychological; certain ideas that are totally irrational to a healthy individual start sounding rational to the addict. Case in point, LOTOJA, riding 206 miles in one day. Spending a couple hours in a day where your average heart beat is greater then 170 bpm. Do this three or four times a week. Spend $80-$100 on one pair of shorts. Burn so many calories such that food intake becomes a chore. Does any of this sound rational in the slightest? Finally, as with other addictions, continuous bicycle use leads to longer, more intense use to achieve the same high. For a few months I was content with my 18.3 mile loop three times a week; no longer does that do the trick. I now have to do a 25.4 mile loop three times a week to get the same high. I’m sure I missing some of the unseen effects.

So there you have it, full disclosure. I am addicted to bicycle use with some pretty dire effects to my physical and emotional health. How do I feel about my addiction? I wouldn’t change a thing!

Backpacking Bryce Canyon

I went to Bryce Canyon with my good friend, Christopher, to go on my obligatory summer backpacking trip. I think that backcountry backpacking is my favorite thing in the world. We left Sandy at 4AM to ensure that we caught the park shuttle to the other end of the park, to Rainbow Point. The plan was to take the ‘Under the Rim trail.’ This is a one-way 23-mile trail that extends through the entire park, almost. The problem with backpacking here is water; there are only two reliable water sources, that is the two places we camped. The first day was rather simple; from where we were dropped off, at Rainbow Point, we only had to go 4 miles to our campsite (Iron Spring). Shortly after we got there it started to rain. Considering that we were in the desert, it was a pretty healthy rain but short lived. There was a reliable water source, Iron Spring, but it had lots of minerals and silt in it the clogged the filter rather quickly. We hiked up close to the top of the ‘rim’ where there were some pretty neat rock formations. We then went down to where we heard water flowing and followed it up to find what I’m sure was the head of Iron Spring. Unfortunately fires are not permitted in the park so when night came we didn’t spend too much time talking, we went to bed rather quickly as it got fairly cold. A strange thing that I will not forget is the quiet that accompanied the night at Iron Spring. There was no wind, no crickets, no noise at all; it was kind of eerie.

The second day was a lot more grueling than either of us had expected. We had to go 13 miles to our next campsite. We had thought, ‘yeah, we can do 13 miles, no problem.’ It was almost as if we had failed to figure in the fact that we had 35 LBS on our backs. We started around 10:30 AM and didn’t get to camp until 7:30 PM. This stretch of the trail had no water to speak of. We had filled all our water at Iron Spring, it turned out that that amount was barely enough to carry us through the 13 mile trek. We were dead when we finally made it to the second campsite, Yellow Creek. There was another group at this site from Belgium. Luckily the ‘creek’ was right next to camp. After we filled our water bottles, we cooked dinner, setup camp, and went to bed. It was a very grueling day and we were exhausted!

The next day we took it easy and stayed around camp to allow our bodies to recover. We spent time talking, diverting the creek, damning the creek, bathing, etc. At one point we decided to follow the creek upstream. Well, the bugs up river had another idea. We got to one point where then coordinated an attack on us, it was horrible! So we quickly got away from the creek and made our way back to camp. The next day we packed up camp and walked the last six miles to Bryce Point. This was a very different portion of the trail. We went through a desolate sagebrush field, thick scrub oak, and finally a steep accent to Bryce Point. The accent was neat as we finally got to see those strange hoodoo formations that Bryce Canyon is famous for. We made it back, took the shuttle to the car, and drove back to Sandy.

All and all, it was a great backpacking trip. This was very different from the backpacking trips that I usually take as it was in the desert. Luckily it was the high desert so it never got too hot. Christopher and I had a great time together; it was just the two of us. I’ll have to find a new partner for next year as Christopher will be on his mission.

View from Rainbow Point, the start. We followed those cliffs that you see in the distance.

Starting Down the trail. (me)

Starting Down the trail. (Topher)

Pink cliffs, no pink ladies though :(

A cool chasm!

On the trail.

Starting to get in the hoodoos on the last trail.

Getting to the end of the trail. (me)

Getting to the end of the trail. (Topher)

Getting to the end of the trail. (random hoodoos)

6-27-2011 Bike Ride

As my last ride for my three week vacation to Utah I did my 'Mama Bear' loop. 'Baby Bear', my 20 mile loop, was getting all my attention. Mama bear is almost 28 miles. Maybe in August I'll introduce you to 'Papa Bear'. Side Note: according to this site, I am burning as many calories on this ride as a healthy individual exercising three times a week should intake. No wonder I am ALWAYS hungry!!

6-20-2011 Bike Ride

I am now biking three times a week. I usually do my 18 mile loop. If you include my ride into lab its actually 20 miles.

ACA 2011

I spent this last week in New Orleans at the American Crystallographic Association (ACA) conference. I was there with my awesome lab mate and new roommate, Christopher. This is the same conference that I went to in Chicago last year. The conference happened two months earlier this year due to the international crystallography conference that happens this summer. The ACA conference is meant to get scientist in the crystallography community together to share their research. This really is a prime way to learn what others are doing, develop ‘research relationships’, and bounce ideas off one another. I feel that these conferences are an essential component to scientific discovery.

Getting to New Orleans happened to be a bigger deal than one would have anticipated, but we had a few lucky breaks and got there only a few hours later than expected. When Jane, my PI, picked us up, it was raining very heavily, the kind of rain that simply doesn’t occur in Utah. Getting out to the car was enough to get my feet soaked wet. On the way to the airport we drove out of the storm and I thought we were going to be in the air soon enough. When we got situated at our gate another portion of the storm rolled in and set up camp over the airport. Pretty soon they had to delay all in-coming and out-going flights due to lightning. The airport was shutdown for about three hours. It quickly became apparent that we would miss our connection. The agents were very busy trying to help passengers sort out their missed connections so we had to wait quite a while to talk to sort out our connection. The agent

confirmed us on a flight from Atlanta to New Orleans in the morning and put us on stand-by for a flight later that night. She told us that Atlanta was already backed up from the same storm system and we’d likely have to spend the night at the Atlanta airport. Long story short, a very nice agent in Atlanta put us on priority stand-by and we made it onto the later flight. We were in New Orleans only a few hours later than scheduled.

I have to be honest; in my humble opinion New Orleans is not as cool as Chicago but pretty neat nonetheless. My biggest complaint was that the city seemed dirty to me. Christopher had a fair point when he mentioned that it was an old city and old cities generally looked dirtier. They had garbage bins on every curb, which I thought was odd. As I looked around though I realized how cramped the city was, especially in the French quarter, where else could they put the trash? The food was great. We went to Red Fish Grill on Bourbon Street, it was by far the best food we had there. We also went to Johnny’s Po Boys where I got the New Orleans original, the Muffaletta (See picture). Of course, we had gumbo and jambalaya.

Red Fish Grill

Johnny's Muffaletta

On the last night we were there we went to a Thai restaurant which was on the opposite side of the French Quarter from our Hotel. We walked down Royal Street all the way to the restaurant. My pineapple-fried rice was yummy. When we were done we decided to walk the entirety of Bourbon Street. By this time the sun was setting and things were getting started on Bourbon Street. Suffice it to say that two devout Christian men were educated. The live music in every bar was neat, live music is always pretty cool. Other then that I have nothing good to say about that street. I can say that women are prettier with cloths on and the adult superstore does NOT sell adults. I don’t plan on making that stroll ever again.

We spent most days in the conference listening to talks and interacting with other scientists and even a few legends in the field. Wednesday we decided to go to the local aquarium, right next to the Mississippi River. After going to look at the river and take a few pictures we went into the aquarium. It was a very neat attraction! I could go on about the variety of colorful fish, the sea otters or even the penguin exhibit. I’ll spare you and tell you my favorite creature there, the jellyfish! They were small but I think I like them best that way. They move so gracefully and are simply beautiful.

On Thursday I had to give a fifteen-minute talk. I talked mainly about recommendations made by a task force that Jane was on. It was on validation of crystallographic structures deposited in the PDB. I also talked about a new tool that I created called MolProbity Compare, which allows the user to compare two validation reports of two different models. Unfortunately my talk was in the afternoon on the last day, a lot of the participants are gone by that time. Further, there were other sessions that were happening simultaneously that I had to compete with. I frankly was surprised at the 10-15 people in the room who listened to my talk.

There you have it, New Orleans in a nutshell.

New Orleans

At the end of this month I will be venturing to New Orleans to attend the American Crystallographic Association conference. This is a research conference that happens every year; last year that I attended the same conference in Chicago. The main goal of these kinds of conferences is to disseminate knowledge gained through research. This dissemination is usually done through two kinds of presentations, oral presentations and poster presentations. Just about every student that goes presents a poster. If the research that you propose to present is good and of general interest they will pick you to give a talk.

So, how does one propose a research presentation? That is done by submitting an abstract, which is a short synopsis of your research. My lab mate and I submitted our abstracts a few months back. The conference organizers will typically tell you well in advance that your abstract has been accepted and what kind of presentation you’d be giving, which is a poster presentation 95% of the time. It occurred to me last week that the conference was right around the corner and I had yet to hear from the conference. I got worried when someone informed me that they had tried to email me but it had not gone through. Was I sent an email from the conference but didn’t get it? So I sent an email to the conference organizers explaining my predicament.

While I was waiting for a reply, I went to the conference website and noticed that they had published the conference program. If my abstract had been accepted my name would appear in my program. The list of posters was quite extensive, as such, I searched for my name using the browser’s find function. My name came up not under posters but rather under talks. That’s right, I have been assigned to give a talk.
The talk will be 15 minutes long and I will mostly be talking about work that my mentor did. She was on an international task force whose job was to recommend validation methodologies that will be incorporated into the Protein Data Bank (PDB). The PDB is where all published protein models have to be deposited. Everybody is interested in this topic as everybody wants to have a model that looks good and thus will p ass as a good structure using the new validation techniques. I will also be presenting some of my research.

So there you have it, my exciting news. As a side note, I will be in Utah from June 29 to July 19. I cannot wait to see everybody!

Die tree, die!!

The past month has been pretty quiet. I have been getting ready for my initial committee meeting. This meeting is deigned to introduce my committee to myself but more importantly my project. For those who are unfamiliar with the process of getting a PhD this committee is made up of faculty members who will follow me throughout my tenure as a graduate student. Their job is to ensure that I am doing the things that I need to receive a PhD. Finally, at my dissertation defense I ‘defend’ my research to them. To get ready for the initial meeting one must prepare a short summary on my the research that I propose doing and prepare a very short presentation. I have also, of course, been continuing with my research. As usual in research, it is going slowly but going nonetheless.

This week I had the opportunity to go see a performance put on by the Young Ambassadors of BYU. Their program included singing and dancing. The performance followed the ideal life; childhood, adolescence, marriage, adulthood and growing old. They were very good at what they did…suffice it to say it reminded me of Saturday’s Warriors.

Unfortunately, the only biking that I get in is my daily commute to and from lab. I’d like tpo do more but another activity has taken priority, working in the yard. Yesterday I started to take down a tree in the backyard. A vicious vine was overtaking this tree, it was a matter of time before the vine would kill the tree. It also was in the way any time that I wanted to take out the garbage or mow the lawn. I was only able to take down half of it as there was only so much room in our yard waste bins; I’ll do the rest next week.

That’s it for now.

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.

Lawrence Berkley Labratory

This last week I was in Berkeley California at the Phenix developer’s workshop. Phenix is a software package whose goal it is to advance the automation of macromolecular structure determination. The workshop was held on the grounds of Lawrence Berkeley National Laboratory, situated on the hillside right above the campus of UC Berkeley. I liked the area a lot. As I showed in my last post, the lab has its own resident turkeys. Further, black-tailed deer can be seen further up the hill. The mornings were awesome, they reminded me of mornings in Utah. I think it is because there was a large hill immediately to the east, thus the direct-sunlight wasn’t seen until later in the morning.

While at the workshop I had the opportunity to work with lots of cool people. I truly enjoyed working with my Phenix friends. My PI had a great idea for a research project that I could tackle to be part of my dissertation project. While there I told a colleague about the project and he suggested a way in which I might accomplish the project, he even had code that advanced my project by several steps! However, this has mad me keenly aware of the fact that I have a ton to learn!! It is good though as this gives me direction whereas before I feel I was lacking a clear direction.

The fight home was my first red-eye. Its very difficult to fly east with the time change. Anyway, we left San Francisco at midnight, Pacific Time, and landed in Durham around 9:30 AM, Eastern Time. I find it hard to sleep in a bed let alone on an airplane. Needless to say, I did not sleep on the plane, one of only a handful on the flight. By the time I got home I was, surprisingly, wide-awake. I didn’t go to bed until 11PM that night making 39 consecutive hours without sleep, a new record for me!

Anyway, it was a great trip and I am looking forward to the next Phenix workshop this fall here at Duke.

LBL

What, may you ask, is LBL? Well, I'm here to not only tell you but show you also. LBL stands for Lawrence Berkeley Laboratory. It is on the campus of the University of California, you know, the one in Berkeley. This happens to be where I am right now, for a collaboration workshop. This workshop, which is held every six months, rotates between here, Duke, and Cambridge. I may have more to say when all is said and done at the end of the week. Until then, enjoy these pictures I managed to get with my phone this morning.

Looking down onto the campus from LBL.

The LBL guest house.

Trees and the overcast sky.

Resident turkeys.

A resident.

A random building.

Look out on the bay.

Opposition in all Things

So, from my last post it looks like I promised to write a new post a few weeks ago. Obviously, this did not happen. I have been quite busy with life in general; taxes, research, class, TA duties, and yard work…you get the idea. Yup, you heard right, I said yard work. It has been warm as of late and I have been turning the soil over in my garden. I meant to get early crops in but time was not to be found. I have been really busy in the lab, learning a new programming language, Java. Programming is quite simple, all you are doing is telling the computer to take input from the user and if that input is some action, such as a right-click, then do thing A. There are really only a very few primitive commands that you need to make a program, quite amazing. I have been busy doing other school activities too, class and TA responsibilities (A.K.A. thermodynamics and grading).

You may ask then, what do I do when I am not in lab or doing the school thing? I do bike but not a lot. When I get done with the day I usually go home trying ever so hard to keep school and lab things behind. One thing I do not do when I get home is sit in front of the TV; I can’t stand TV. Instead I read. Since I am a great believer in opposition in all things, I have chosen to read Stephen Hawking’s ‘A brief History of Time.’ How does this introduce opposition? Quit simply really. You see, as a student of structural biology I am working in a world where measurements are made on the angstrom scale. An angstrom is a whole magnitude of order less than a nanometer! Certainly almost all have heard of a nanometer but that doesn’t mean that you have an intuition of how small that is. Let me try to instill some intuition about the nanometer and then the angstrom.

I will assume you are familiar with the length of a meter. One tenth of a meter is a decimeter (or 0.1 meter) and one tenth of a decimeter (or one one-hundredth of a meter if you’d like) is a centimeter (or 0.01 meter). Approximately 2.5 centimeters is the length of an inch (this will be the only reference I will give to the cockamamie U.S. convention of length measurement). So, a tenth of a tenth of a meter is a centimeter. Are you with me so far? Good. A tenth of a centimeter is a millimeter (or a tenth of a tenth of a tenth of a meter or 0.001 meter). Now think of a human hair, the average size of which is a tenth of a millimeter, pretty small!

This will be the last reference of anything observable to the human eye as anything smaller is fairly difficult, if not impossible, to see with the naked eye. We’ve come a long way but the millimeter is not even half way to the angstrom! Go down three orders of magnitude from a millimeter and you’ll arrive at the micrometer (or 0.000 001 meter). Lets jump down ANOTHER three orders of magnitude, we’ve now arrived at the nanometer (or 0.000 000 001 meter). Recap: three orders of magnitude below meter is millimeter, three more orders down is the micrometer, and three orders down still is the nanometer. Now we go just one order of magnitude below the nanometer and we finally arrive at the angstrom (1 angstrom = 0. 000 000 000 1meter). I hope you followed; my goal was simply to underscore the fact that I am constantly thinking in these small lengths within my research and schoolwork too.

I have yet to answer the question that brought on that rant, why does reading ‘A Brief History of Time’ introduce opposition at all into my life? Well, you see, being a theoretical astrophysicist and all Stephen Hawking tends to write about length scales that are, quite literally, astronomically big. It is nice to come home and peek into another world where people are always thinking about large distances rather than small distances, as I do.

Opposition is like taking a break from a grueling run. It does not only feels amazing but is essential for physical and mental health. Did I just compare my research to a grueling run? Yes, yes I did. I’m ok with that.

My eventful 2011 thus far

So, I have had quite the eventful 2011. It all commenced on the first day of 2011. I wrote about my Christmas break and that first day of 2011 on January 2. I have chosen to share it now because I was foolishly paranoid that this somehow could have been used in court. Here the delayed post from January 2:

I have just returned from my holiday break. It all started on Sunday December 19, when my good friend Jeremy and I went up to my bother’s home in Virginia. The next morning we flew out to Salt Lake where we surprised my family. I had my Aunt Pam pick us up from the airport then we went to lunch; I had Pam invite my parents and my grandma to lunch. Jeremy and I were waiting at the back of the restaurant. As soon as everyone was seated the host informed us and we walked in. The reaction from everyone was priceless. My parents were so excited; it was great. That night we went to surprise my two sisters’ and their families. Jonna and her family were excited to see me; despite being called a brat, I enjoyed the surprise. We then went to surprise Becky. Becky’s reaction was the best! She was laying on the couch, eyes glued to the television, which allowed me to sneak up on her, putting my face next to her face. At this point she proceeded to jump on the couch, like a four-year-old, screaming, “I KNEW IT!” several times in a row. She then hugged me with her arms AND legs causing me to fall back on the couch. Very special moments indeed.

I was initially worried that Jeremy would be rather board at my house but surprisingly we kept pretty busy. We went skiing, well I did, Jeremy snowboarded, it was his first time! We did that on three of the days. We also went to the movies twice and went on two hikes. Not to mention all the Christmas parties. It was really great to spend time with my family during the holidays.

The puzzle that we did at my parent's home in Utah

Jeremy and I on top of the Majestic lift at Brighton Utah

Jeremy an me with Big Willow in the background

We flew out and in to Washington DC. When we landed Shane and Becky picked us up. We took Jeremy to Union Station to catch a train north. I stayed with my Shane’s family and spent a few days spending time with them. We went to see a movie; besides that we simply hung out at home and did puzzles, which I loved. On new years day I stated to drive back to Durham. It was a rather uneventful trip until I stopped for dinner and to get gas. When I was getting onto the freeway, on a rather curvy onramp, I started to slide and my tires hit the soft shoulder and I ran into an embankment. When all was said and done I had no front bumper and some sort of fuel was leaking out from beneath to car rendering it un-drivable. There were no witnesses but a passer by called the Virginia State Troopers. They called a tow truck, filed a report, cited me with reckless driving (I have to go to court Feb 8), and they then dropped me off at the Days Inn where I had a VERY restless night. Be at ease, I was not hurt at all but my car is in pretty bad shape. Now we have to wait until the business week to start to see what the insurance company will do. What a joy. Not the best way to end the trip but it is what it is.

Here is the rest of the story:

As explained in my January 2 post I was in an accident in a little town in southern Virginia, South Hill to be exact. The next five weeks were hell, nevertheless an awesome learning experience. Not only did I have to deal with my wrecked car but I was also was on a new medication for my dystonia that had horrible side effects, the worst of which was playing with my cognition and emotions. Suffice it to say this fact compounded the hellish nature of the situation. NOTE: I have since weaned off the medications and will no longer take ANY meds unless something drastic changes.

Now to my car and dealing with my insurance company. I called and reported a claim the same night of my accident. I was assigned to an agent in Massachusetts; why I was not given a local agent is beyond me. The agent got back to me fairly quickly. I explained where my car was and that the mom and pop body shop didn’t have the capacity to make a proper estimate; she needed to send an adjuster. Luckily, the insurance covered a rental, which I picked up later on in the first week. The body shop told me that an adjuster did come by and look at my car but that they needed the adjuster’s estimate and report. Two weeks after the accident I got a message on my phone from my adjuster indicating that they had made a check out to Honda Finance and me for the amount of the repairs. I was confused as I was under the impression that the insurance company was suppose to be working with and ultimately paying the body shop not me. I promptly called my adjuster and, as usual, she didn’t pick up the phone and I left a message telling her that I was confused as to why she sent me the check and why she was not sending the body shop the requisite documents to repair my car. After leaving two or three messages like this without a response I was getting frustrated.

I finally had my dad and the body shop, as well as myself, call on the same day and leave her a message, one from each of us, demanding that she send the documents and get back to us. I guess that was the trick; she sent the adjuster’s report and the body shop started to work on my car. It took two weeks to make all of the repairs. Last week I heard from the body shop and they told me that the car would be ready by the weekend. As such, I decided to go and cash the check that the insurance company had sent me. However, since the check was made out to Honda Finance AND myself, I could not cash the check. After going to the Honda dealership I found out the necessary hoops that I needed to jump through to get the money to the body shop. Long story short, I learned that Honda Finance had no interest in my car and that the insurance company needed to cut me a new check with the proper lean holder. After signing a legal document saying that I authorized the said body shop to repair my car, which they had already done, they sent a check straight to the owners of the shop. This put considerable delays in getting my car back. I was to turn in my rental before I had my car. After arguing with the insurance company they grudgingly agreed to extend the rental for three days. It was very apparent that the check would not get to the body shop in time and I would have to go without a car for a day or two. Normally this would not be a big deal but I had to be in Virginia for my hearing on the reckless driving charge. The insurance refused to extend the rental even though their incompetence caused the delay. I will tell you about my hearing in a future post but I had to pay for a rental so that I could get up there. The day of my hearing the repair shop got the check and the next day, this past Wednesday, I was able to retrieve my car.

I am so sorry to vent but it helps ☺. Plus my siblings want to know what happened. There it is in sufficient detail. I will post a more pleasant post tomorrow. Have a wonderful day!