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!

North Carolina is not a Continuous Function

Hi folks. I am sincerely sorry for not updating my blog sooner. It so happens that I have actually written a post explaining the fun I had during Christmas and the event that ended the break and the fun. However, out of paranoia, perhaps, I am choosing to wait to share that post until later in February.

This semester, besides research, I am taking on another tutorial-based course (statistical thermodynamics) and I am a TA for another course (macromolecular structure). The tutorial class is by choice where as the TA assignment is not. At Duke, graduate students in my department are required to TA one course. For some odd reason they assigned me to TA the macromolecular course (this was written in the most sarcastic tone…believe me). The TA duties, as of now, revolve around copying class handouts and grading the weekly assignments. Grading is not fun; no wonder math professors higher undergraduate math majors to grade assignments!

Statistical thermodynamics on the other hand is an absolutely fascinating class. Since it is tutorial based, the class, all 5 of us, get to dictate how fast we go. We are now taking time to get the proper mathematical foundation needed for the rest of the course. For me, this means learning math that I have not had before, differential equations. To learn such things I have found that reviewing basic calculus requisite. Luckily, calculus is roughly analogous to riding a bike; once you learn it a quick review brings it all back again. I find math amazing and fascinating. As I learn these new mathematical methods I keep on thinking, ‘You know if I wasn’t doing this PhD gig, I‘d totally go for a second bachelors in math’.

We are learning how to find an extreme on a 3D-surface; how cool is that?!! I know you’re all dying to know, ‘How can I do that?!’ I highly recommend you watch a video or two on Lagrange multipliers; there are a few good ones on youtube.

So Friday night Jeremy put an idea in my head by asking, ‘Road trip?’ You see, we both had no plans for Saturday and the weather was supposed to be phenomenal. I has heard of this place called ‘Hanging Rock’ here in NC and had always wanted to go. I went home and researched the matter. After finding out the Hanging Rock was a state park with numerous hiking trails a mere 2 hours away, I was sold. At 11 PM I texted Jeremy and we planned on a 7 AM departure. The drive there was uneventful. The state park was beautiful, complete with a lake, campsites, hiking trails and a hidden pond. The terrain was relatively rugged; mind you, the ‘relative’ term refers to the state of North Carolina. In fact, that is where the title of my post comes from; ‘North Carolina is not a Continuous Function’. This is analogous to saying that there are actually cliffs in NC. We hiked to the highest point in the park; a tad over a whopping 2500 feet (sarcastic tone). At the top there is an old fire-watch tower; it’s pretty cool. Jeremy brought his camera and I’ll be sure to post the pictures ASAP. Until then, enjoy Jeremy’s panoramic video from atop the watch tower.

Hanging Rock Video

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...

(Not me:) but a great picture nonetheless)

So these last couple of weeks I have been writing and re-writing a couple of grants, as I said in my last post. Well, I finally got the first draft of the NIH grant done and will get comments on it back from my PI tomorrow. That’s pretty much it for school.

Yesterday I went on a 50 mile bike ride. I did the exact same loop a few weeks ago and surprisingly felt fine afterwards, save a few sore muscles. This time however was different. I was doing fine until I hit mile 35. I was running out of gas with fifteen more miles to go. I had no choice but to keep on going, so that is what I did. It was difficult and I had a very hard time constantly pedaling (for those who are unfamiliar with road biking that is what you do, pedal constantly). At one point in those last fifteen miles I stopped and got off the bike to stretch. A car was kind enough to pull over and ensure that I was alright. I told her that I was just taking a break. I got back on my bike and rode the rest of the way in. I think that the main problem was that I had not prepared nutritionally before hand and did not bring sufficient food for my travels.

As I often like to do, I will liken this bike ride to life. This journey we are on in mortality can provide us with stretches that are particularly hard to deal with. The hardships may come in a variety of forms. Whatever the case may be, I believe that, for at a few of those trials, they come because of our lack of preparation. I need only to cite the parable of the ten virgins to illustrate the point. Some tough days can be anticipated; these can usually be prepared for to one degree or another. However, some rough times may sneak upon us unawares. But let it be known that these trials can be prepared for just as those we anticipate by living the Gospel as well as we know how to. We need to keep it simple as Elder Ballard emphasized in the last YSA fireside. Read the scriptures, pray, ponder, re-read the conference talks, serve, repent etc. The simple things are what matters most. Some may say, “But I have issue A.” This matters not. Indeed ‘issue A’ may be very difficult but the simplicity of the gospel is not and, with patience, the with the simplicity of the Gospen ‘issue A’ will be overcome.

First we must have faith, “hope for things which are not seen, which are true” (Alma 32:21). Second we must repent. Third we must keep our covenants. Finally we muse seek the Spirit. The Spirit will tell us all things what we should do (2 Nephi 27:3). Simplicity is the key, no if, and or buts about it. The truth is that I simply did not prepare properly for the bike ride; I needed more food, my body was screaming, “I need carbohydrates.” The question then becomes, “What is my spirit screaming for?” Praying and pondering for the answer to this question, no matter if we are a smooth or rough spot, and seeking out that which is revealed will increase our endurance during the rough times in our lives.

One of my favorite scriptures. It doesn’t make a bad song either :)

“In a little wrath I hid my face from thee for a moment; but with everlasting kindness will I have mercy on thee, saith the Lord thy Redeemer.” Isaiah 54:8

Grants and a Road Trip

My research has been put on hold as I attempt to get funding through two federal agencies, the NSF (the National Science Foundation) and the NIH (National Institute of Heath). Both these require a grant proposal detailing what I propose to research as a graduate student. The NSF proposal requires a personal statement, previous research essay, and the research proposal, each are confined to two pages. The NIH grant requires a one page detailing the specific aims of the project and a six page research plan. I am done with the NSF one, I’ve gotten pretty good at doing these as this is my third time doing it and my last year of eligibility. The NIH grant is new to me and require much more detail on what I propose. This one is due on in three weeks. So for the next three weeks I’ll be attempting to write a well conceived proposal.

Last Friday my friend, Tennyson, and I took a road trip to the Cherokee reservation in western North Carolina; up in the mountains. It took the whole day as it takes 4-5 hours to bet to the reservation. It turned out that we left way too late and had to reschedule his appointment for latter in the afternoon. This turned out to be a good thing as we were able to stop in Ashville, a town I’ve wanted to visit since I’ve arrived in NC. It is a hippie town with a lot of small shops and restaurants, this is where we ate lunch. We ate at an Indian buffet; it was very good. We then traveled to the reservation. We had to climb a high pass where there was a heavy dusting of snow. We took the trip mainly so Tennyson could go visit the dentist on the reservation. It was great to see the reservation and the mountains of NC. I hope to go back there again.

Yesterday I took a bike ride; it was spectacular as the temperatures were in the sixties and the leaves were at their peak, reds, yellows, and oranges. On my ride I stopped to visit Dave and Jane at their home, which was nicely tucked away in the woods. Their home is very unique, like noting I have seen before. They have a central foundation up from which a steel pole emenates. The main house cantilevers from that pole in a circle. They then have an addition roughly in the shape of a soccer ball, very cool! Unfortunately I have no pictures to show.

These pictures are from the aforementioned road trip. Enjoy.

This was at a cool shop we stopped at that had a bunch of crafts and home-made foods.

NC Snow!

Costume shop, Ashville, NC.

Ashville, NC.

Halloween

This weekend was, as wee all know, the great holiday where we celebrate scary things and eating an abundance of candy. For those unfamiliar with this holiday one usually dresses up for the festivities. As such I dressed up as a zombie cyclist. Enjoy the pictures!

Zach

Wardrobe malfunction. Me and Hayley

Zach, me, Jeremy