Review on "Naturally Obsessed" from LabLit

I found this to be a great review on the documentary "Naturally Obsessed."  Let me know what you think of the author's opinions!

Link: Tell it true: Naturally Obsessed

Reflection on "Naturally Obsessed"

             I discovered the unique and sometimes altogether crazy band titled The Flaming Lips during my senior year of high school.  One particular thing that attracted me to this great band is that they caught their big break during an episode of Beavis and Butthead.  When Dr. Cooper told me that the documentary we were watching contained a song by them, I thought that at least the film had one positive going for it.  Surprisingly, I thoroughly enjoyed the flow of the "Naturally Obsessed:  The Making of a Scientist" and the honest message about graduate school that it portrayed.  While I find research to be interesting, I have some serious doubts about if I would be happy doing it for a career.

            One aspect that made this documentary personally enjoyable is that I am currently conducting biochemical.  Even though my research is more laid back and primitive than the work being performed by Dr. Shapiro’s team, I had a basic understanding of their goals and problems they were encountering along the way.  Also, my own personal failures in the lab made it easy to relate with the emotions that the characters encountered throughout the filming.  It would be interesting to hear what a person with no science background thought about the film.  While this may be a strong statement, I believe one must have spent time performing independent research that sought to answer something unknown to understand the characters on a deeper level.  For someone like Dr. Cooper who has performed biomedical research, this movie must have struck a major chord and brought back many memories about life in a lab.

            Even though Robert Townley was probably the most interesting graduate student to follow due to his quirky mannerisms, I felt a strong emotional attraction to the student named Kil.  The way he carried himself and invested a great deal of time and effort into his research reminded me of myself.  Also similar to me, the research failures appeared to stay with him for quite some time after they occurred.  One saying of his that I enjoyed was “We don’t learn anything from success.  Rather, we learn from failures.”  He did not say this statement as if to lecture others, but instead, it appeared he mentioned it to try and convince himself of its truth.  While I also hold this motto to be valid, it is difficult for me to come to terms with the reality of the statement.  Watching Kil struggle throughout the filming of the documentary caused me to have second thoughts about being able to succeed in an M.D./Ph.D. program.

            These concerns about my happiness in an M.D./Ph.D. program are not related to being bored with the research.  This is because I find the premise of delving into the unknown to be fascinating.  My downfall in research would likely be caused by investing too much time into my work and making my failures personal. It has always been my intention to start a family and raise my children to the best of my abilities at a relatively young age.  While others may be able to balance a family and graduate school remarkably well, I do not have the skill set to accomplish both tasks at once.  This is the most prevalent reason for having doubts about entering a dual degree program.  I also seriously wonder if my psyche could withstand the constant failures that are inevitable in research.  To circumvent this problem, I would need the proper advisor to encourage me along the way.  Still, something is leading me to toss around the possibility of pursuing both M.D. and Ph.D. degrees.

            Overall, I would strongly recommend this movie to anyone who has even a basic background in the sciences.  It gives a detailed look into the lives of the people who make the discoveries that we read about in the popular media daily.  As far as people considering entering graduate school, it is essential to be exposed to this film.  This is because it gives a look into some of the trying times that will be ahead.  Personally, it caused me to seriously wonder if I possess the skills required to succeed in research.

Documentary watched:
Rifkind, R. & Rifkind, C. (Directors).  (2009).  Naturally Obsessed:  The Making of a Scientist.  Public Broadcasting Service.

Reaction to Opinion Articles

            Memories of my first afternoon in Dr. Cooper’s lab are imprinted firmly in my mind.  We had just finished discussing some of the details in my project, and she asked me if I would like to get started. I hesitantly responded “yes” even though I was already overwhelmed with trying to digest the basic concept behind my project.  With Dr. Cooper by my side, we proceeded to set up digests using restriction endonucleases on a plasmid vector.  However, at the time, I was basically just putting small amounts of liquid into tubes without any idea of what was going on.  I left the lab that afternoon with a sick feeling in my stomach because of how little I understood.  I kept thinking about how painful my research experience was going to be if I remained in this state of ignorance.  Martin Schwartz admits in his article “The Importance of Stupidity in Scientific Research” that “feeling stupid” in the lab is not for everyone, but for those who can cope with it, it is a driving source towards making scientific discoveries.  After some humbling experiences, I have become more comfortable with continually saying “I don’t know” in the lab, and I would like to continue conducting scientific research in the future.

            As Schwartz mentions in his article about many young students, I too was attracted to science because of the ease with which it came to me.  Up until my junior year, I thought I had they key to being successful in the sciences because I could memorize a great deal of information.  This approach may be fine in the classroom, but it quickly fails a person in the lab.  One must use critical thinking skills against obstacles that seem insurmountable at times.  The humbling moments far outweigh the times when everything seems to come together.

            This state of ignorance is inevitable when conducting worthwhile scientific research.  Gone are the days of following “cookbook” lab protocols in class to find an expected outcome.  One spends time performing research to answer the unknown questions in life.   For a long period of time, I did not believe I could handle the feeling of continually being in the dark with my own research project.  However, even managing small breakthroughs provided me with a euphoric feeling and ignited a desire to proceed further into the unknown.

            Conducting research at whatever medical school I attend will be vastly different than my experiences at a small institution like Loras College.  Loras is a sort of comfort zone for me where I know every face that I encounter and do not hesitate to ask questions.  Just the thought of working in a new lab with intense students is enough to make me perspire.  For this reason, I am thankful for encountering Jonathan W. Yewdell’s two-part article titled “How to Succeed in Science.”  I found the first portion of the article to relate most to my current situation because it discusses what to expect when first beginning research at a new institution.  His helpful hints have given me an idea of what type of research experience will be most compatible with my personality and goals.

            The most helpful section dealt with how to choose a mentor.  This is because not every mentor will be as nurturing and understanding as Dr. Cooper.  I am not concerned about an advisor who expects a great amount of time commitment on my part because I will give my best effort.  Most importantly, I desire someone whose research goals match mine and is approachable.  My ultimate goal is to be a better practicing physician as a result of my lab work, and I will be looking for someone who is supportive of this objective.

            My critical thinking skills have grown exponentially since I began working in Dr. Cooper’s lab.  This safe environment has given me a taste of what research in graduate school will entail.  While I know there will be many difficult times where I feel absolutely lost, I look forward to trying to answer some of the unknown questions in the health sciences.

Literature Cited:

Schwartz, M. A.  (2008).  The importance of stupidity in scientific research.  Journal of Cell Science.  121. 1771.

Yewdell, J. W.  (2008).  How to succeed in science:  a concise guide for young biomedical scientists.  Part I:  taking the plunge.  Molecular Cell Biology.  9.  413-416.

This Week's Music

I've decided to share some songs/artists that I'm really into this week in lab.  If only Pandora didn't have a forty hour limit per month...

Smashing Pumpkins- Cherub Rock, Today, and Tonight, Tonight
The Band (This one's for you, Casey and Brennan)
The Format (So unknown, so great)
Death Cab for Cutie  (Except for that crappy song from the Twilight movie.  Boo to selling out!)
Marshall Tucker Band
Radiohead (First time I've actually listened to The Bends and Ok Computer completely through, and it was amazing)
Bon Iver (Anyone who produces an album in a cabin in Wisconsin is cool with me)

Shadowing Opportunity

For a small school, I believe Loras College offers many unique research opportunities for undergrad students.  However, rarely does one get the opportunity to witness these projects on personal basis.  This afternoon I had the privilege of shadowing Cara Marie while she was working in Dr. Schnee’s lab.  The primary goal of Cara Marie’s research is to determine the effect of cadmium exposure on the mating patterns of fruit flies (Drosophila melanogaster).  I now have a profound level of respect for the research the students in Dr. Schnee’s lab are performing.  Still, I am thankful for the research I am conducting.

By the time I shadowed Cara Marie, I had already witnessed two of her presentations on her work, so I had a basic idea of how she was spending the J-term.  However, following her around really helped to answer some of my lingering questions about the project.  Cara Marie was already working diligently by the time I joined her during the afternoon, so I was thrown right into the mix. 

The most interesting part of the afternoon was observing the behavior of a male fly that was exposed to a .75 M concentration of cadmium when it was mixed with a female fly that did not have any cadmium exposure.  These flies were combined in a vile that contained neither food nor water.  Cara Marie said one can tell the identity of each fly apart from the other because male flies have a dark spot on the abdomen, but I was not easily able to perform this task.  We began timing the courting pattern as soon as the flies were together at the top of the vile.  The female fruit fly seemed uninterested and continually left the male’s company.  After around fifteen minutes of watching the flies they had been courting each other for nearly ten minutes.  At one point during the courtship, the male fly began to undertake an activity known as preening.  This is a cleaning procedure that the fly performs to prepare itself for mating.  Interestingly, Cara Marie commented that the male fly appeared to be noticing that the female was uninterested in him, and the male fly may have been trying to clean off any residual cadmium.  The observation was concluded after the thirty minute mark, and at this point the flies still had yet to mate.  Dr. Schnee commented that around twenty-five similar watches are required to make any type of conclusion about the mating behavior of the flies.

While we were observing the courtship between the two flies, Cara Marie broke down a typical day for her and some of the necessary preparations for her work.  I could not believe the amount of time she spends just making sure she had enough flies to work with.  Observing the flies was very tedious and not extremely exciting to me, but Cara Marie was completely engrossed in what was occurring before us.  Also, because she is working with a higher level of organism than the bacteria that I am used to, she is on the flies’ time to a certain extent.  It definitely requires a patient personality to perform animal observations, and Cara Marie fits this mold well.  One could sense the level of excitement she had once the flies began to display any type of ritual courtship mannerisms. Her enthusiasm was enjoyable to witness.

Even though I greatly enjoyed my shadowing opportunity, I am glad to be working in a cell biology lab.  I do not believe I have the required patience to observe the behavior of fruit flies for an entire day.  Still, I find the overall premise of the research to be interesting, and I look forward to viewing Cara Marie’s results at the end of J-term.

Reaction to the First Week of Research

            It is somewhat difficult to believe that I have been doing research for over a year now.  I can still remember the first conversation with my research advisor, Dr. Cooper, vividly.  She asked me if I had ever thought about a career in research.  I quite coldly proclaimed that under no circumstances would I want to conduct research for a living.  Working in a lab was viewed by me at this time as little more than a requirement to graduate and something to put on my resume for medical school.  However, this opinion began to slowly change as I invested more time and effort into my project.  I became so passionate about conducting research that I even applied for an MD/PhD position at one of the medical schools I was accepted into.  Being enrolled in this course has only reinforced my desire to continue to conduct scientific research in the future.  Still, I cannot neglect my passion for working with patients in a clinical setting.

            The change in my feelings about working in a lab was not just the result of a revelation one day.  Rather, it came about after spending an increasing amount of time in the lab and conducting research in conjunction with taking an introductory biochemistry course.  Part of the reason I was frustrated with my first couple of months in the lab was because I did not really understand the theories behind the procedures.  As I took cell biology and biochemistry, things started to click, and I became able to anticipate future challenges and think critically about necessary changes in my work.  I would strongly encourage students who are just starting to perform research to stay positive even when things appear bleak.  The outlook will become progressively rosier as you begin to master specific protocols and procedures related to your field.  Even if you do not particularly enjoy research, at least you can say you gave it a valiant attempt.

            I can honestly say that this course has only increased my appreciation for a career in research.  One of the most pleasant parts is working in close proximity with other students who have similar projects.  Brainstorming and helping one another makes the day go very quickly and provides a sense of support.  Another thing I enjoy is that this is the only course we are currently taking.  In the past, I often ran into difficulties when trying to schedule research around my class schedule.  Now, I am capable of working at a pace that allows for accomplishing a great deal in one day.  An aspect that is somewhat of a pain is waiting to receive results and orders that have been sent off to outside companies/labs.  Trying to find projects to remain busy with that only take a short amount of time can be quite challenging.

            It has become rather clear through this research experience that I would like to perform clinical studies in the future.  I still find my work to be exciting, but this enthusiasm would likely start to wane after a while due to a lack of interaction with patients on a regular basis.  I remain convinced that I can be of the most benefit to society by working in a clinical setting as a physician.  Luckily, there are many great teaching hospitals that will enable me to combine my liking for research and clinical medicine. 

            I still find it amazing how far my appreciation for research has come.  This course has been a great introduction for the next step in a career in research.  I look forward to continuing research in the future because it will make me a better physician and allow me stay up-to-date in the advances in science.

Reaction to "A Brief History of the Hypothesis"

            One of my earliest recollections of science courses from elementary school is of being introduced to the term “hypothesis.”  At this age, it was simply defined as an educated guess, and we were told a hypothesis is imperative to conduct scientific studies.  My classmates and I then proceeded to carry out a rudimentary experiment observing a caterpillar undergo a metamorphosis to a butterfly.  It is still a commonly held belief amongst most of society that, for an experiment to be of any merit, it must contain a hypothesis. However, as Glass and Hall (2008) explain in their article about the history of the term hypothesis, a significant amount of research today takes place without a well-defined hypothesis.  Rather, the studies are primarily driven by inductive reasoning that aims to answer questions that the researchers have.  While this method has its shortcomings, I find it to be the most practical way to practice in the future as a physician.

            A central argument that some philosophers put forth against inductive reasoning is the idea that we cannot predict future events (Glass & Hall, 2008).  It is true that humans cannot be absolutely sure that something will occur in the future.  However, it would be foolish to view happenings as stand-alone events that have no connection to the past or future.  We are handcuffed by the unknown, but we must act as though events will occur in a similar manner in the future.  A practical application of this belief is a physician treating a patient with a disease in the same way as he or she treated a patient with the same disease in the past.  One should stay open to the idea that the future may stray from the past, and make the appropriate adaptations if this occurs.

            As was mentioned by Glass and Hall (2008) and discussed in depth in class, probability helps defend inductive reasoning.  Still, there exists the chance of any event occurring in the future.  A statistical principle known as the Law of Large Numbers states that, as the number of experiments held increases, we become closer to obtaining the true probability of that event occurring.  Therefore, the probability of an event can essentially be taken as zero if it has not happened after countless tests.

            Other fields of study may be different, but formulating a concrete hypothesis often does not apply to biology.  As one of the students mentioned during discussion, there are usually a tremendous amount of variables present to account for in biological research.  One must resort to observing a system repeatedly and try to make general conclusions that try to explain the results.  This is a great example of inductive reasoning in action.

            An interesting claim that the article makes is that hypotheses are not relevant today due partially to the abundance of information we have accumulated.  Instead of formulating hypotheses to try to falsify, the authors suggest that researchers search for solid answers to questions.  My brief research experience has been based around the latter of these two options.  In fact, it would be foreign for me to try and function under the premise of the first option.  Trying to answers may not be the absolute method to conduct scientific research, but it will likely remain as the primary school of thought in the foreseeable future.

Literature Cited:

Glass, D. J. & Hall, N.  (2008).  A Brief History of the Hypothesis.  Cell, 134, 378-381.

Site-Directed Mutagenesis Technique

            The original goal for my research project was to create a ligation independent cloning (LIC) vector from the plasmid pcDNA3.1+.  The basic outline of this project consisted of: digesting the plasmid using the restriction endonucleases KpnI and HindIII, annealing pre-designed oligonucleotides that were complimentary to the nucleotide overhangs on the digested vector, and combining the digested plasmid and annealed insert through the use of the enzyme T4 DNA ligase to create recombinant DNA.  This novel plasmid could then be used to perform ligation independent cloning, which I will not describe in depth in this blog post.  While the outline appears fairly straightforward in principle, I was unable successfully create my vector after nearly a year of performing research.
            It was decided to try and create a ligation independent cloning vector using a different starting plasmid, and pEGFP-C1 was chosen to fill this role.  The benefit of using the vector pEGFP-C1 is that it contains the gene for enhanced green fluorescent protein.  Cells that express this vector with the desired gene are then tagged with a fluorescent protein, and this helps with the ease of observing the transfected cells.

            There is one problem that exists with trying to use pEGFP-C1 for my LIC vector instead of pcDNA3.1+.  To activate the LIC vector, it must be cut with a restriction endonuclease at the location where the gene will be inserted.  We designed this region to be a cut site for the enzyme SacII.  This is a logical choice for the vector pcDNA3.1+ because it does not contain any other sequences where SacII can digest.  pEGFP-C1, however, contains one other SacII cut site besides the one found in the insert.  This would create difficulties when trying to use the vector because SacII would be able to make two cuts every time the LIC vector derived from pEGFP-C1 is digested.  The LIC vector with both sites digested would be made effectively inactive.

             A technique to circumvent this problem with the created LIC vector is site-directed mutagenesis.  QuickChange Lightning Site-directed Mutagenesis is described in Figure 1 (Stratagene, 2007).  The objective of this technique is to change the nucleotide sequence of the non-insert SacII restriction site.  By changing the nucleotides in this region, the sequence-dependent SacII will no longer be able to cleave the DNA molecule at this location.

            The key to site-directed mutagenesis is in designing oligonucleotides that contain the desired mutation to serve as complimentary primers to the plasmid of interest.  In order for the primers to pair with their complimentary regions by abrupt cooling, the double stranded plasmid must first be denatured with heating.  A heat resistant DNA polymerase then extends the 3’ end of each primer.  DNA ligase links the 5’ end with the 3’ of the DNA strand containing the designed primer to create a circular DNA molecule.  Another round of similar replication must be performed to produce the double-stranded plasmid with the desired mutation. This process can be repeated with the assistance of a thermocycler to create a large quantity of mutated plasmid.

            The original plasmid, or parental DNA, that remains after the replication cycles can be cleaved and inactivated through the use of the restriction enzyme DpnI.  This enzyme has the capability of cleaving methylated and hemimethylated DNA.  The parental DNA is isolated from E. coli which methylates its DNA (Stratagene, 2007).  The mutated DNA will not be susceptible to cleavage by DpnI because it has been produced in vitro without any methylation.  The plasmid of interest can be harvested by transforming it into competent cells. 

Literature Cited:

Stratagene.  (2007).  QuickChange Lightning Site-Directed Mutagenesis Kit.  Retrieved from http://www.qcbio.com/stratagene/210518.pdf

Figure 1.  QuickChange Lightning Site-Directed Mutagenesis makes use of primers that contain the desired mutation.  The primers were designed to change a SacII restriction site into a non-cut site.  The figure is provided in Stratagene’s protocol for the QuickChange Lightning Site-Directed Mutagenesis.