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!