Tag Archives: RF2016-Week1


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As someone with limited exposure to programming and coding, knowing that I’d be working with MATLAB for eight weeks worried me. I wanted to finish B-SURF with a greater understanding about how science is produced, and I was afraid that my inexperience would hinder my progress. Interestingly, MATLAB has already taught me some of my most important lessons in science.

  1. Learn by trial and error: This is basically how I’ve learned everything. Whenever I need to execute a function, I search for the type of command I want on mathworks.com/help/matlab/index.html, and experiment until it works. Watching an error message disappear is one of the most satisfying feelings.
  2. Collaboration is important: Luckily for me, some of the other undergraduates in the lab have several years of programming experience. Working with them is always extremely helpful. I spent most of the other day trying to optimize a script, and one of the undergraduates rewrote the entire code in 10 minutes. Thanks, Alan.
  3. Science can take on many forms: Throughout high school I always held a notion that scientific research was a bunch of people in white lab coats watching over boiling, colorful liquids or looking through a microscope. Little did I know that my first research experience would involve a lot of MATLAB, and few white lab coats.

I’m much more optimistic at the end of week one, and I didn’t expect to enjoy my work as much as I do. I’m excited for the work I’m doing, and am eager to see where my project goes.



Baby Steps of an Inexperienced Researcher

When I started my first week at BSURF, I felt very excited and eager to finally take part in a research project where I could explore and learn the different aspects of doing science. My only experience with biological research has been the lab component of Bio201 class, so I was a little nervous and worried about whether I could pull this off. First week in Kuo lab, I learned a lot more than I expected. I started with attending the lab meeting where lab members were presenting their data and analyzing it with Dr. Chay Kuo, my principal investigator. I would like to share something Dr. Kuo said during the meeting (as far as I remember) and I really liked: “Don’t be frustrated when you get a result you didn’t anticipate. Be excited, because you will learn new things with your unexpected results, not the expected ones.” I think this accurately demonstrates the paths scientists go through when they make breakthroughs and I set this as my first guideline when doing research.

In this summer, I will be conducting a mutagenesis project where I will try to determine which site of a protein is accountable for degradation of that protein in ependymal cells of the brain. I will mutate the protein multiple times and hopefully find the right site by the end of the program. During the first week, Khadar, my supervisor, taught me how to prepare agar plates, do bacterial transformation and some other basic lab techniques which will be very important when I start my mutagenesis project next week.

Besides those techniques, essentially I did a lot of reading regarding the literature related to our research and at first it seemed somewhat boring. But then I realized how important it is to understand what really is going on. In order to understand my role in the project and contribute to it, to find solutions to the problems we encounter, I should have a very good grasp of the experiments conducted, the techniques used , why, where and when they are used and which results could they provide to answer our questions. Sure, learning to follow protocols, pipetting, doing PCRs flawlessly are all very important since they will lead to correct results, but I think I can learn doing those things over time, as I do them repetitively and learn from my mistakes each time I make one. What I really want to learn this summer, besides perfecting my basic lab skills, is to think like a scientist. In the long term, I want to be able to ask the right questions and make the right decisions to control the direction of the research. So far, I found everything I looked for and I hope to continue in Kuo lab  not for just 2 months but for years.

On a side note, I  took some Turkish Delights to the lab and especially Dr. Kuo loved it. So, as long as I keep offering him more Turkish delights, I think I’ll have a secure spot in this lab.

From Theory to Practice

Having completed a year at Duke filled with science classes including biology labs and papers on genetics, I thought I had a decent grasp on what research involved. After a week of preparing an especially large experiment (studying germination in Arabidopsis thaliana) in the Donohue Lab, it’s quite clear that a few pages of a paper cannot fully convey the level of dedication needed for researchers to perform experiments. What may be a single sentence in the methods section of a paper may involve months of planning and work. My first day in lab, I was told that over 2300 plates of agar needed to be prepared for the upcoming experiment. At the time, I was oblivious to the hours of mixing, microwaving, pouring, and bubble-popping that such a number entailed. However, it will surely be exciting to witness the progression of the plates throughout the experiment and the results that they bear, as well as actually participate in the process myself.

Overall, I hope to discover what research is like for myself. Although I hear about it every day from my professors, other students, and papers during the school year, I’ve already realized this week that nothing can really compare to your own experiences. Since I’m rather (read: greatly, ridiculously, hopelessly, etc.) undecided about my future and weather I want to pursue research (genomics, bioinformatics, or something else?) or engineering (biomedical or electrical?) or most preferably some combination of the two, I hope that this experience will help give me some sort of indication. As I’ve already begun to see from the speakers this week—and hope to continue to see in the remainder of the program—scientific research isn’t so cleanly cut along divisions. It can involve multiple disciplines and require an array of skills that necessitates cooperation among scientists and those from other departments, which I hope to continue to hear about in the future.

While the research projects themselves are certainly a big part of this program, I expect that the weeks to come will offer even more insight into the world of research. Whether listening to seminars from Duke faculty, discussing projects both formally and informally with other students, forming connections with our mentors and hearing how they got to where they are today, or just learning general skills (both in and out of the lab), I’m sure that this summer will be a remarkable experience day in and day out.

My “Selfish” Expectations

     Going in lab always gives me peace of mind: during my first year at Duke, whenever I felt stressed, I would just go to the plant genetics lab that I was volunteering in, get a PCR done, do a transformation, or run some assays. I stayed in lab for three hours before my interview for BSURF, and I spent an entire day in lab before my ECE final. It was always only when I had gloves on and pipets in hand that I could truly appreciate the elegance of biology, forget everything else, and feel the thrill of doing something I love.
     And then there comes BSURF. Surprisingly, the first day I walked into the Jiang lab in the Department of Medial Genetics, all I felt was excitement. No sweat in my hand. No stutter in my speech. Yes, plant genetics was cool – but this summer, I get to work on actual humans. A box of DNA samples from real, human patients already awaited me in the refrigerator. And looking around, there were all these fancy machines that I had never used or seen before. As my mentor introduced all the machines to me one by one – real-time PCR machine, ultracentrifuge, etc. – I felt more and more awestruck. I kept picturing how amazed I would feel if I could operate these machines on my own. I know I will get beautiful results and ugly ones, but either way, I marvel at how people had discovered all these ways to visualize and quantify the teeny tiny cell world. The machines are elegant. The whole lab is scenic. And I easily get addicted to scenic places with elegant designs.
     What’s even more exciting is that during the eight weeks, besides lab bench, I will also be doing a lot of computational work such as DNA sequence comparison and analysis. This is a new skill to me and I am very excited to learn. In the past week, I’ve already learned to how to find the cDNA of a gene, how to find different isoforms of a given protein-coding sequence, and how to design primers for PCR. I believe these are fundamental to any research related to genetics, and they will help me become a more independent researcher.
     Looking ahead, I don’t expect to understand the biochemistry of the operating mechanisms of all the fancy machines in lab, but I do want to get an idea of their functions, and how they help with research. I don’t expect to find or confirm the genetic causes of some neurological diseases, but I do want to get to learn as much as possible about the research of other people in lab, who are actually finding these causes. I don’t even expect my experiments to work all the time, but I just want to enjoy the view of lab everyday. I want to enjoy the machines humming, the “click” when a pipet tip is discarded and the attentive eyes of scientists. These expectations might sound a little selfish – I’m not even expecting to contribute to the field even the slightest amount – but I really can’t wait spend my eight weeks appreciating the elegance of biology and find my peace of mind within it.
Update: Here is a picture of me working (?) in the Jiang lab.

Work, Think, and Act like a Scientist

A lot of words characterized my first week here:

  • I was excited to begin my first real research experience.
  • I was nervous that I would make tons of mistakes.
  • I was appreciative for everything everyone has done so far – Dr. Grunwald for making this program possible, Jason for supporting us and giving advice, Duke professors for sharing their research experiences, my secondary mentor Matt for guiding and teaching me, and the Poss Lab for letting me work with them this summer!

Conducting real research is a lot different from learning science in a classroom. When I work in the Poss Lab, I’m not conducting experiments everyone has done before in their organic chemistry classes. Real research is open-ended. There are no clear, numbered steps and I never know what I’m going to get. Thus, over the summer, I hope to be able to work, think, and act like a scientist. What does this mean?

I hope to work like a scientist. I hope to be able to understand what real research is like and to gain a deeper understanding of the scientific process at play. I already feel like I have learned a great deal this week. Whether it was learning new lab techniques (I did my first PCR this week…and my second…third…I lost count) as well as understanding the fundamental concepts behind regeneration (what the Poss Lab focuses on), I hope to not just follow protocols and to transfer colorless liquids with a pipette, but to truly understand what is going on. I also expect to make mistakes, in fact I already have. I don’t expect all my experiments to be successful- whether it was my DNA not running properly on gel or my bacterial transformation failing. What’s important, however, are the valuable takeaways in learning from my mistakes.

I also hope to think like a scientist. I hope to always be constantly asking questions (thank you to Matt for patiently answering the endless amount of questions I had) and to be learning something new every day.

Lastly, I hope to act like a scientist. I am excited to continue to build upon my genuine interest for biology. Not only will I be doing what I enjoy every day, I will also be delving deeper into regeneration research as I hope to contribute as a member of a team of researchers at the Poss Lab as well as build long lasting connections with these talented scientists.

This first week has already been everything and more and I look forward to explore what’s to come in the next 7 weeks.

What I learned in Boating School is…


“Floor it?”

While of course I’m not enrolled in Mrs. Puff’s Boating School, this week me and Spongebob have shared this expression on more than one occasion. Specifically, whenever someone in my lab asks me a question. God forbid it’s related to math or chemistry, which it almost always is. A few days ago, my mentor asked me about the weight of water. Easy, right? Wrong. I spent about five minutes babbling and starting sentences that I never finished. “Isn’t it…Well, like it’s…I learned this before…” The ironic thing is that I knew the density of water, but I didn’t trust myself enough to believe that I was right.

The one major thing that I want to gain from this program is confidence. I hope to get to a point where I’m not afraid to answer a question whether I know the answer or not. After reflecting on what I’ve done this week in lab, it seemed silly to me that I spent 5 days of basically non-stop practice pipetting. But then I also remember how clumsy and scared of messing up I was on day one. Now, after disposing of my own weight’s worth of pipette tips, I am not only better from a technique standpoint, but I also have a lot more faith in my ability to use pipettes. Big or small, multi or single-channel, clip tip or not… You get the idea. And while learning about how to use various pipettes is an undeniably useful skill, so far, the biggest thing that I’ve learned in Dr. Haynes’ Boating School is that I am surrounded by amazing people who are always willing to help me when I don’t know something.  Unfortunately, I think my parents are expecting me to return home with a Nobel Prize but I think I’ll just return home and not sweat when I’m asked a question.