Reflection (and on SMART GOALS)

Well, Winterim is over and I won't be visiting the Willey Lab for a little while, but I still remember everything that happened. The good, the bad, and the teaching moments that came to me because of this Independent Study have made me realize that it will be a long, hard road till I become a doctor. However, if it's something I'm really interested in (which I am) it will be worth it, and there are programs that I can get into that would make that road even easier. This Winterim really helped me start thinking about what I really want to be in life.

That being said, not did I enjoy the Winterim, but I feel that I have learned a ton! In the beginning, I struggled to barely explain what I did to Mr. Meinecke. Now, I can explain it to random people at Winterim Fair. All because of how I paid attention and picked up on the things Tom, Doctor Willey, Erin, etc told me.

As for my goals:

1. I listened, and I applied what I heard in the lab. That in and of itself is a massive achievement as I normally don't listen as well as I should. I put my ego at the door and took every piece of advice that people were willing to give. As a result, I have learned a LOT and I can tell that I have (along with friends) .

2. For the first time, I actually worked when people weren't watching. Normally, I am pretty lax with my attention to detail, but during this Winterim, I stayed focused even when I wasn't being directly monitored. I did this because I wanted for the data I generated to be consistant and of high quality. Not only can you tell from my anecdotal evidence, but the consistency of my data shows that I stayed focused.

3. I did waste some things in the lab, which I felt pretty bad about at first. Multiple times, I did little mistakes that would have caused contamination, so I had to throw them out. However, Tom stated that it was important that I realize that I had messed up and prevent contamination. For the majority of the time I spent in the lab, I kept my consumption of resources to as low as possible.

I hope you have enjoyed my blog. If you have any questions, email me at 14twoo@mvcds.org

DAY 16 Saying HI

Today just to make sure everything was in place, I stopped by at the lab and said "hi" to Doctor Willey. He invited me back next summer and next winterim, and I might take him up on those offers. I thanked him for opportunity and went over some concepts, then left. Time to get ready for WINTERIM FAIR BABY!

DAY 15 SAD :(

Today was my last day. To make up for the sadness that I was feeling, I brought in some Wixey Bakery Donuts (which the office loved and probably helped my evaluation). My data collection went well and I finally started my Qiagen Column sample.

However, throughout the day, I got this feeling in my gut. It was a really weird feeling because I started thinking about how I had to go back to... school... ew... I wanted to be in the lab working, gossiping, and generating data. I didn't want to leave at 3, but I had to.  I said goodbye to everyone for now, but I'm sure that I want to go back there at some point and work. NO DOUBT.

Day 14 ALL in PERSPECTIVE

WELL. Today I ran my first two test and I looked at the results. I was super discouraged because I have mixed up which sample were which; furthermore, even when I sorted that out, my data still wasn't too solid. I was so frustrated with this. I have worked really hard and been doing a lot of tests. I didn't want to just start making mistakes this massively. So I went to Tom, defeated, preparing for a verbal lashing about how terrible I was at running tests.

He looked at my data and casually said, "Oh, looks like you got some Primer Dimers". Essentially the reaction went wrong and there's nothing I can do about it. And he looked over my data and thought it looked good and explained that it was pretty solid still. I started to feel better, but then he took it a step better.

He told me that I was doing a very good job (he later called me brilliant) and that I was producing very good data, something that undergrads, Masters students, and even Ph.Ds struggle with. Basically, I should just relax because there isn't really a "wrong answer". I was on cloud 9.

Day 13 More Progress

I ran more tests today and Tom again commented that my data was looking solid. I've gotten so much more productive and so much more comfortable, so I am producing data at a substantially higher rate. I just tentatively reached the halfway mark today, and I should be able to do the other half in the next three days! Hopefully I'll have enough data to draw a good conclusion for Winterim Fair.

ALSO
Speaking of Winterim Fair, I need to come up with a triboard for next Tuesday. I don't need a physical one, but I'm more interested in what should I tell people. I'm going to ask Doctor Willey and other people in the office about how I should do it so that I can effectively convey what I did for 3 weeks.

Day 12 The Catch

Today was another good day. I came in early and was extra productive. In the morning, I ran 2 PCR samples (I usually run 1 a day). I began to format my data and Tom approved of the way I did it. After looking at my data, he was impressed by my data. By tomorrow morning, I should have finished all of my data for the Trizol method and could start the Qaigen samples and HOPEFULLY finish by Monday. I felt really good about myself!

HOPEFULLY THIS CONTINUES!

Day 11 Day Off!

So UT was closed today because of Veteran's Day, but I am going to talk about last Thursday.

I said there would be more analysis and here it is.

In the lab, I really like how autonomous you get to be. Basically, you chose the problem you want to solve then come up with a way to solve it. The good part is that "failure" isn't bad as it can sometimes still yield something else. Also, I liked the atmosphere and the people, but also the subject matter.

In contrast, I kind of liked the clinic because you get to deal with problemed people and solve their ailments. The talking with people and making a bond with complete strangers seems really awesome. Combined with a medical background, I could have a blast with it. The age that seems the best would be children since I love kids, but I will see with time.

Day 10... What more?

So today, I finally got to finish extracting RNA. It took roughly the entire morning, but front the cells that I grew up, I got RNA! This afternoon I took the RNA and used reverse transcriptase to make cDNA, which I could then use to run my experiments on.

Speaking of which, the experiments are going well, but there's still a ton of them that I have to do :/ I need to be very productive next week if I want to finish my project. I'm up to the challenge!

I can't believe two weeks are already gone. I'm going to continue to work hard the rest of Winterim!

Day 9 ...Awkward...

Today was a very interesting day. In the morning, I was in the final step of setting up electrophoresis to get the amounts of the certain genes, and I tripped with the sample in my hand. It fell on the ground and the samples left the wells. I had to start all over, which was really annoying and aggravating. I did eventually get it right and get some really good data. I should have finished ALL of the Trizol method cDNA by tomorrow. WOOT WOOT! Then I just have to do the cDNA from the Qaigen and I'll be done!

Also, I have taken my cell cultures and broken them down. Instead of being in a colony like they had been for the entire time, they've been detached from the vial and most were discarded. The only thing that remains is roughly 640000 cells that I will extract RNA from tomorrow and use Reverse Transcriptase to make cDNA!!!

About the title, today, Danny and I went to Grand Rounds. Usually, there is an interesting speaker and free pizza: DOUBLE WIN. But today, the speaker was terrible. He was SO BAD that the other attending doctors actually declared that his protocol was malpractice. Essentially, for twenty minutes, six doctors debated proper protocols for hyponatremia (lack of sodium in blood) in front of Danny, 50+ med students, and me... VERY AWKWARD!

Day 8 Something New

This will be a pretty short post because my internet will disconnect me any second now. Today was something different. In the morning, I did my normal experiments. Not only did they turn out kind of "wonky", I had to redo the experiment. However, Tom wasn't displeased; instead, he was happy because it meant I would get more accurate data.

After I finished with that, I got to go to the clinic where Doctor Willey works. I shadowed him and the 3 other fellows and residents that are under him. I REALLY liked what they did, and I instantly thought it could be something that I thrive at (perhaps at a pediatric setting?). More analysis to come!

Day 7 Definitely a Tuesday

Today wasn't spectatular, but it was a productive day. I finally did my calculations for the ratio of ERCC5 to ACTB for both the RNA extraction methods. They were 6 and 4 per thousand for the Trizol and Qaigen methods respectively. Multiple people will then do this test and someone will take all our data to draw a conclusion (hopefully giving me some credit). So now, instead of measuring one gene at time, I'm measuring seven genes at time. Tom trust my data (enough) to do this, which is reaffirming.

I PCR'ed the 9 total samples (7 genes, an internal standard, and a negative control H2O) and that's all of my office work.

Tom and I spent a lot of time just talking about life paths and dealing with cancer. He said that we will probably never "cure" cancer. We will get to the point where we can manage it where we can greatly prolong length of lives, but not completely kill every single cancer cell at later (3rd and 4th) stages. Kind of a downer, but still, Tom said that there are two big reasons to do this job: one because it's massive problem solving at a molecular level (something I like) and because you're making people's lives better. You're helping others while truly fulfilling yourself, which is something I want to.

Day 6 Cells EVERYWHERE!

So today, I saw Mr. Boehm. He and I talked about what I was doing and I did a basic orientation for him in the lab. Tom and Mr. Boehm then talked about me (infront of me which was awkward), but Tom said that I was a very good student and that I had "the proper amount of sarcasm/humor needed to be a scientist". I grinned a lot. Another question that Mr. Boehm raised was what was the point of my experiments. He was wondering if I was just doing an experiment that they knew the results, which wouldn't be too important. On the contrary, Tom stated that I was preforming experiments for things they didn't know the answers to and they were possibly going to use my data in the future. WOOT!

After that, I did my calculations for the experiments from Friday. I struggled with them a little more than I usually do, but eventually I made sense of them. Again, WOOT!

But the best part of today was that I got to look at the cell cultures I made. They had undergone large amounts of Mitosis and covered roughly 77.738685% of the one side of cell container. So that they wouldn't over grow, Erin and I split them into two different containers. Next, I will extract the RNA from one container's cells, while I take a majority of the cells from the other container and destroy them. Then, with the remaining 10% of original cells, I will freeze them in liquid nitrogen (which is roughly -230 degrees C YIKESSS!) for later use.

Look at all my cells replicating: 

Reflection

"on your goals?

1. Are you listening more actively?

2. It seems like you must be concentrating well since your labs are going well. 

3. How's this going? Have you broken anything?

Mr. Boehm"

1. I think I've done a lot more listening than I normally do. Not only that, I can tell that I have learned A LOT!

2. When working in the lab, I've been playing strict attention to details and as you said, my data has been pretty solid as a result.

3. So that I'm not bring wasteful, I made the 3rd goal. I hadn't broken anything and only a few times I have wasted things.

Overall, I think I am making good progress at accomplishing my goals.

Day 5 Weekend, Holler!

My tests went well!! Woot! When Tom and I analyzed the data from yesterday's experiment, the data was within 5% of what it should have been. With that, he set up more complex experiments that I did in the same way. However, I didn't have enough time to discuss the data, so I don't know exactly how to describe why I did the tests (don't worry that's coming). However, he quickly look over it and thought it looked pretty sound.

Also, my cell cultures are going well. I could see cells that fixed to the bottle I had placed them in. Interestingly, I caught one in the middle of mitosis, so there were 2 nuclei in 1 cell (I thought that was cool). 

Day 4 Synergy!

Today was a really hard day. First thing in the morning, Tom drilled me on what I had done yesterday. We went over why we had done things and why they are important. Then, he had me write up my own procedure for another round of PCR and Electrophoresis. That wasn't too hard, but then he had me set up the experiment and did it all by my self. It was pretty hard keeping track of everything and we will see how well I did tomorrow. If I did well, Tom will turn me loose to do 15 more genes.... If I didn't, more practice. No pressure :/

But, another facet of my education in the lab happened today. Erin, another associate of Doctor Willey, taught me how to make cell cultures. Essentially, I'm growing more and more copies of the same cell so I can harvest the RNA to plug into the other experiment I've been doing. I'm starting to go full circle. Hopefully, I did things right!

Day 3 PROGRESS!!!

Today was a really good day and I'm excited to tell about it. Flashback to yesterday, right as Tom and I were about to start my first experiment, Doctor Willey realized that they had to do something very important for this article they are about to publish. We stopped and Tom did his thing. Flashforward to today, for the whole morning, Tom and I set up proper dilatations of DNA so that we could titrate properly (essentially we are just trying to find how many of the unknown molecules we have based upon a set ratio of fluorescence). Then, Tom walked through the experiment, doing all of the pipetting (which is a pain) and explaining why he was doing each step and telling little helpful tidbits of lab procedure. He then had me do the exact same thing back to him. Luckily, I pick up on things quickly, but just the pipetting caused my muscles to shake and nearly spasm. It looked so much easier when he did it! But, he did say that I did a very good job (even better for my first time... EVER). We put the samples we had made up into the PCR machine. We then went to lunch. Yes, I know. Very anticlimactic.

We then came back (I did faster than he because he got stuck at Fricker's) and ran the amplified samples through a fancy and expensive (worth over $30000,  I didn't even think about touching it) machine that performed electrophoresis to see how long the strands are. Just to give a frame of reference, our DNA in each cell has billions and billions of base pairs. The genes we were interested in have roughly 500. Then, based upon different dilutions, we could set up proportions to see roughly the amount of molecules from this test. We are testing to see if two different extraction methods have RNA (therefore cDNA) that are in the same proportion. 

....You should be confused. I sure was, and if you have any questions, please ask!

Below are pictures of where I worked:

PCR machine:

My little comfy station: 

Quotes from Emporer of all Maladies

Tom gave me a really good book about cancer called "Emporer of all Maladies" by Siddhartha Mukherjee, and it has some interesting descriptions of cancer for people who don't know too much about cancer:

"Cell division allows us as organisms to grow, to adapt, to recover, to repair- to live. And distorted and unleashed, it allows cancer cells to grow, to flourish, to adapt, to recover, and to repair- to live at the cost of our living. Cancer cells grow faster, adapt better. They are more perfect versions of ourselves." (6)

"Cancer is an expansionist disease; it invades through tissues, sets up colonies in hostile landscape, seeking "sanctuary" in one organ and then immigrating to another. It lives desperately, inventively, fiercely, territorially, cannily, and defensively-at time, as if teaching us how to survive. To confront cancer is to encounter a parallel species, one perhaps more adapted to survival than even we are.

This image- of cancer as our desperate, malevolent, contemporary doppelgänger- is so haunting because it is at least partly true. A cancer cell is an astonishing perversion of the normal cell. Cancer is a phenomenally successful invader and colonizer in part because itnexploitsnthe very features that make us successful as a species or as an organism." (36)

Wow. It's amazing we even stand a chance.

Project WOOT!

So, I talked to Tom and Dr. Willey and they came up with the experiment I'm going to partake in. They think they have developed a biomarker for detecting lung cancer based upon 14 genes found in RNA. However, there currently two types of RNA extraction for this test: Trizol reagents and Quigen columns. One is more practical for use in most laboratories, but they don't know if they both will read the same gene expression. They want to see if the RNA is the same quality and amount even if the same pieces with extracted from the two different methods.

Revised SMART goals

1. I will listen more than I normally do so I can truly learn from what Doctor  Willey and Tom say.

I will ask questions that will lead me to what I want to know and try to learn more about this subject. I will actively listen to their responses and measure myself based upon how well I can articulate what I learned.

2. When working by myself, I will stay focused on the task at hand, making sure to follow the proper procedure of the lab/activity.

I will remained focused even when working alone. I will pay attention to procedures so that my data is solid. Tom will help me determine if I'm getting good data.

3. When working in the lab, I will be efficient and cautious so that I do not waste or break the expensive materials

I will make sure not to break things so that I'm not wasting the labs resources. I will be able to tell based upon my our lab experiences.

Career?

So Tom and I talked today about what I want to do in life. This was a hard question because... Well... I'm 16 with 80% of my life still ahead of me. He told me about this process at UTMC where I could apply now and automatically get into UT Med School. I would get a lot of scholarships (most likely) and graduate with a medical degree while having a fraction of the debt most graduates would have. One problem:

Going on this path means I won't be making too much money OR have a choice to leave until I am 32ish.... That's a pretty huge commitment. I know I like research and science, but that's an extremely large decision. He also told me that doctors are going to stop making as much money, which could obviously affect my decision.

His biggest advice was to not worry about how much money I make (but make enough to get by) and go for a job I enjoy.

Decisions, decisions :/

Day 1 Morning

So, today is my first day with Doctor Willey at UTMC! It's super cool here and super nerdy here I love it!

We started with basically going over what PCR is. If you don't know what PCR is, it is basically just replicating certain strains of DNA many, many, MANY times so that you can study the DNA sequence more. Click here for more info. I have a pretty good understand of what it is and will hopefully do it again soon.

Thomas (Tom) Blomquist was the primary person I talked to. We talked about a lot of things. Crash course on what cancer is: one cell that has certain mutations that cause it to not cease replicating. I asked why we haven't gotten a cure. Sadly, he stated that since there are so many different types of mutations (at varying locations and degrees), we have an extremely hard time developing a cure. However, it is easier to determine which sequence change causes cancer for younger people. With older people, there have been a countless number of very slight mutations from cell replication. With younger people, they haven't had as much cell replication (therefore mutations), so the sequence is easier to discern.

I've done a lot of reading and this afternoon I'm planning on designing an experiment for Winterim... So YAY! More info to come


Also, here's my school for the next few weeks:

Thad

SMART goals

1. To actively engage in the lab activity that I am assigned so that I am beneficial to whomever I'm working with.
2. To further my understanding about genome sequencing and how it applies to lung cancer and to everyday life.
3. To behave courteously to all the personnel that I have interactions with at UTMC.
4. To effectively accomplish any of the tasks that I am given and report exactly what happened in the lab.