Reflection to "Naturally Obsessed: the Making of a Scientist"

As part of our intensive J-term research we had the privilege of watching the movie “Naturally Obsessed: The Making of a Scientist” which enabled us to virtually experience life in the lab of Lawrence Shapiro at Columbia University. Larry’s lab focuses on determining the 3-dimentional structure of proteins by using x-ray crystallography. This is a very difficult task that requires overproduction of the protein of interest followed by purification and crystallization steps before good data about the structure can be collected.

The film focused on the life and work of three graduate students and their experiences in graduate school. Each student encountered challenges in their research as well as in their personal lives. Even though I have not attended graduate school, I thought that the film provided an excellent representation of what experiences one might have while pursuing a PhD. The film did an excellent job of focusing on several different people so that the viewer could relate, at least in part, to one or more of the characters.  

The most prominent theme in the movie was the concept of learning from failure. The students stressed that though a particular experiment may not work, it would tell them something about how to set up the experiment next time. This intense cycle of trial and error is a common hurdle to making new discoveries experienced by all of the characters in the documentary.

What was particularly interesting was how the students and the professor responded to repeated failure. Some, like Larry, remained optimistic and were eager to try new approaches, while others lost enthusiasm until dropout was inevitable, as was the case with Gabi. Seeing intelligent graduate students struggle in this manner made me think about what type of response I would have to repeated failure. I pictured myself in their shoes. Before this J-term I did not know what it meant to be “productively stupid” (Schwartz, 2008). Now that I have experienced this first hand I still wondered: would I be able to handle the constant disappointments that are inevitable in the world of research?

After watching the entirety of the movie and reflecting upon my experience during the J-term I think that I would be able to handle this type of undertaking if I had the right mentor and was able to adopt the appropriate way of thinking that allowed me to be more objective about the process. Larry was a constant source of honest support for his students. He is quoted for saying, “Our loyalty is to the truth.” This implies that one’s failed experiment should not be discouraging, but rather, teach something about “the truth” that was not known before. Emotion and feelings take a back seat when it comes to science. That is not to say that one cannot be disappointed about a failed experiment or ecstatic when something goes incredibly well. It simply means that everything that you have done, at the end of the day, should be taken in under an objective lens that allows one to see the scientific gains (no matter how small) from that day’s work.

Along with giving me a perspective about the repeated failures that I would be sure to encounter as a graduate student (as well as current experiment failures) this film somehow boosted my motivation to potentially pursuing a research career. Each student had their ups and downs but those that were meant to be there never entirely lost the drive to discover something new and innovative. I realized that there are other components to succeeding in graduate school; it also requires a certain level of talent and creative ability. This is congruent with one of the articles that we had read for this term. Creativity in creating controls is a central part to being an effective scientist (Yewdell, 2008). I have always thought of myself as a creative person but I have never found an avenue in which I was good at expressing this creativity. After developing this new perspective about the intersection of creativity and science I believe that I may have found my creative outlet. However, I have a long way to go before I can start to “paint my own picture” in the scientific world. In order to develop the skills to be an effective scientist many years of intense study are necessary. This film emphasized the importance of persistence, knowledge, and creativity. These all combine to suggest that in order to succeed in science one must always be persistent to make new discoveries and advance their knowledge. This knowledge increases the tools available to the researcher and provides more windows to apply creative thinking which ultimately lead to new discoveries. If I learned one thing from the movie, it is that this cycle of knowledge and new discoveries is aided by creative problem solving skills and is ultimately fueled by persistence and the need to know more.

Works Cited

Rifkind, R., & Rifkind, C. (Producers). (2009). Naturally Obsessed: The Making of a Scientist [Motion Picture].

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

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

Stupidity in Science... And I am not talking about your PI

How much do you know? Top scientists and biomedical researchers are assumed to be all knowing demi-gods in their particular field of interest. However, this assumption does not have merit when the question is phrased: What percent of all that can be known about a particular system do you know? In his article “The importance of stupidity in scientific research,” Martin Schwartz addresses the reality that empirical research is all about wading through the unknown.

The concept of being actively stupid was first introduced to me by last year my research mentor, Dr. Cooper. At first this was a puzzling philosophical undertaking because I had always derived a sense of satisfaction from my academic accomplishments. During the intensive research j-term I truly began to experience this reality first hand. At first, the concept of plunging head first into a pool of the unknown seemed a daunting task that was only suited for the strongest of will. But after a couple weeks of research I have come to realize that the small gains that have been made are incredibly satisfying.

After reading Schwartz’s article I have developed a new perspective of this unique reality. Schwartz suggests that instructors do not spend enough time and energy on teaching students how to be productively stupid. The phrase “productively stupid”, while applied to instructors and their teaching methods, provided me with a new perspective on scientific research. It led me to realize that if I pursue a career in science I have the privilege of acting like a child in that I get to ask tons of interrogative questions that no one has the answer to... yet!

Fortunately or unfortunately (depending upon your interests or perspective) this philosophical approach to applying scientific method is not the only challenge associated with a career in science. Jonathan Yewdell published an article in Nature that provides a sort of ‘protocol’ for success in the scientific community. I really enjoyed reading his article because it was formally structured and informally written. This ironic format is accompanied by his use of humor and wit which do an excellent job of informing young aspiring scientists about some of the most important considerations when choosing a career in biomedical research.

Aspects of his breakdown of the potential pitfalls and potential for success was incredibly helpful to me because I am currently deciding whether to pursue a career in research or a career in clinical medicine. His advice about choosing a school is applicable to both pre medical and research oriented students. The rest of the advice focused on the important components once one was accepted to a PhD program.

Though I have not made a definite decision as to which career path I would like to pursue, as I read his article I found myself imagining a life as a researcher. What school would best fit my interests? How would my PI be? Am I talented enough to actually come up with creative controls and direct my own work? After reading the article I found myself with more questions than answers about which career path I should choose. But at least this is a step forward and has provided me with tools to think about this decision pragmatically. I hope that once I answer some of these questions I will be one step closer to finding my niche in the science community.

Works Consulted

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

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

Yewdell, J. W. (2008). How to succeed in science: a concise guide for young biomedical scientists. Part II: making discoveries. Nature , 1-4.

Refleciton to Blogging

Manny and I are having a blogging party in the caf so I thought that I would blog about it. Thats all...

Reflection of Shadowing Experiences

This week I shadowed two of the other students participating in the intensive J-term research. Cara was working with drosophila and Ryan is trying to synthesize biodiesel from various vegetable oils using enzymes. These two experiments were vastly different from each other and were also different from my project. However, some similarities did exist in the type of critical thinking that is involved in the process of research.

Ryan is working with two different enzymes, porcine and novozym 435. His overall goal is to optimize the yield of biodiesel from vegetable oils using an enzyme. He told me that he chose the porcine enzyme because it was inexpensive and was readily available. The novozym 453 was chosen because previous research had shown it to be a good catalyst for the conversion of soybean oil to biodiesel. However, novozym is priced at over one hundred dollars for a relatively small sample and it is not economically feasible to use something like this in industry (which is the real world application of Ryan’s project). I asked Ryan about this and he explained that a more efficient process was to immobilize the enzyme onto a larger substance so that it can be recovered after the reaction, rather than being discarded.

When I observed Ryan he had just immobilized the porcine enzyme one to celite. While I am not sure of the exact protocol he used liquid nitrogen to flash freeze the enzyme and the celite to immobilize porcine onto the celite. The water from the reaction mixture was removed at room temperature using a vacuum evaporator.

While this is an entirely different project I did notice a similarity in this portion of his research. Ryan has chosen a less expensive enzyme to use to test the efficiency of the immobilization process before he applies this technique to his novozym. This is very similar to testing the viability of the primers that I ordered. Before running a PCR on PACSIN 2 with the Phusion enzyme, I test to see if my new primers are effective at initiating the replication by testing with a less expensive enzyme, PAQ 5000.

While I was talking to Ryan I asked if he would employ some type of positive control to see if his porcine was adhered to the celite. He told me that he was not sure how he would do that and we discussed possibilities for several minutes. This is much like the work in the DNA lab. Often times we bounce ideas off of each other and ask others for assistance. I suggested looking at the known enzymatic functions of porcine and testing it on one of these substrates.

While Ryan was working on a completely different project I was able to see these similarities in critical thinking strategies. It is good to know that all of our projects relate to some degree. I look forward to hearing about his findings this week!

Cara has been examining the effects of exposure to high concentrations of cadmium and its effect on the breeding patterns of the flies. She has implemented the use of several controls to ensure that her results are viable. Her protocols involve mating virgin flies which ensures that there are no behavioral changes due to the female being already fertilized. She also uses a media for some flies that do not contain any cadmium. This is significant because it provides a control in a statistical analysis of the experimental trials. I did not ask Cara but I assume that once all of the data collection is done she will use several chi-squared tests that will compare the control trials against the experimental trials.

While at first glance our experiments do not appear to have similarities there is one main connection between our two projects. Her project involves concentrations that have never been tried before. Though these concentrations have never been tried before, she did mention that lower levels of cadmium exposure have been tested in previous research. Thus, the questions that arise in her work stem from examining previous research. This is very similar to my research because many of my protocols are adapted from previous research that has optimized certain types of reactions. Both of our projects involve adapting protocols from previous work which makes our research more productive and provides us with the opportunity to ask new questions and seek new answers.

It was a privilege to shadow both Ryan and Cara. They were very informative and were eager to answer questions about their research. After shadowing them I have gained a greater appreciation of research as a whole because I realize that, though the project goal may be different, the process for developing new questions and seeking new answers is congruent through different fields of work.

J-term Intensive Research Has Changed my Opinion of what it Means to be a Research Scientist

Preconceived notions about scientists and research had me led to believe that in order to be a good researcher a life of solitude in a lab was inevitable. Stereotypes of the ‘mad scientist’ portray an individual that is overly obsessed with his or her area of study and has little to no personal connections outside of the lab. These stereotypes initially dissuaded my interest in research and led me to believe that if I wanted to have a science career that involved a high level of expertise I was best suited to pursue career that involved interaction with patients and other professionals, such as a doctor. While this is still one of my primary goals, I have gained experience in the lab that has shaped my opinion of life as a research scientist.

Cloning of the zebra fish gene PACSIN 2 has been my primary research focus while at Loras. I have spent nearly three semesters trying to insert PACSIN 2 into pCDNA 3.1⁺ and transform the modified vector into bacterial cells. Initially this appeared to be a fairly linear process that would be used as a tool which is useful in over-expression experiments. Due to my lack of prior experience and the intense nature of my schedule during these semesters I was not able to invest the proper time and energy into the project and began to become pessimistic when I encountered repeated failure at the transformation stage. In order to be able to invest proper time and attention to my project I elected to take the intensive research J-term which would provide me with ample time to accomplish my research goals with the support of my classmates and research advisor.

One week of J-term has passed and my experiences and opinions regarding research are more developed than during the semesters past. Despite the previous roadblocks and obstacles associated with my project I decided to come into the J-term optimistic and prepared to work. The first day of class I was presented with an alternative to the ligation process that I was using in previous semesters. This concept of ligation independent cloning was a stimulating idea and opened my eyes to one of many possibilities to accomplish the same goal.

I was also assigned two other projects that serve as methods to acquire knowledge about the expression patterns of PACSIN 2. These projects fostered teamwork between myself and other members of the research team. The level of cooperation and teamwork that has been required during this term changed my initial stereotype that research is done by an isolationist in a lab.  I have realized that our projects all have something in common and that we work best when we work together. I have very much enjoyed this process and have become very optimistic about my project because I know that the other members of our research team are working toward similar goals and are here to support my research while expecting my support in return. I suspect that research done by professional scientists is performed in this same manner.

While the stereotype of the solitary researcher has changed, my perception that researchers can be literally obsessed with their projects has not changed. During the course of the first week I greatly expanded my knowledge of the PCH family proteins. I found that as the more that I knew regarding my gene as well as the techniques used to study it the more I became drawn into my project.

Now one week has passed and during the second week I find myself constantly thinking about my projects when I am not in the lab. It has become a way of life for the last week and a half, and the more research that I do, the more questions I have. This curiosity fuels my motivation to continue through the term and has led me to be optimistic about a possible research career.

I am currently in the application process to several summer research internships and am very excited to continue to apply myself to this and future projects. This experience has allowed me a window into the life of a researcher and has positively influenced my opinion of research and the process by which it is done. It has also revealed some of the challenges associated with the research process. The life of a full time researcher requires a certain level of obsession with the project that motivates the scientist to stay up to date in their field and put in the long hours that are required to accomplish the project goals.

However, these are not novel revelations about the life of a research scientist. What was most surprising to me was the level of creative and abstract thinking that is required to be an effective researcher. Data interpretation and overcoming project roadblocks require an understanding of the system, patience, and a high level of creative problem solving skills. Prior to this term, I had not thought of this creative capacity as a necessary component to be a scientific researcher.

This unique combination of knowledge, patience, and creativity, requires an individual with an expertise that comes only from experience. I am excited to continue my work for the rest of this term and into the spring semester. This intensive research experience has provided me with a new perspective on the life of a research scientist. I hope to continue research because the more that I know, the more questions that I have and the more interesting the research becomes.

Discussion of a Laboratory Technique: Calcium Phosphate Precipitation on Dictyostelium discoideum

The original goals of my research included examining the physiological functions of PACSIN 2, a PCH protein family member, in zebra fish as well as tagging the protein with green fluorescent protein to examine when and where it is expressed in the developing embryos. The zebra fish has been the animal model that our lab has been using for the past couple of years. Recently my advisor added another model organism to our stocks for study, Dictyostelium discoideum. Dicty is a eukaryotic organism that has many gene analogs that are present in higher eukaryotes (dictybase.org, 2010). Thus it is of particular interest in research because research done on this organism may provide answers to questions about gene and protein function in other organisms.

My first goal in working with this new organism is to determine if the Dicty cells can use the CMV promoter to express a certain protein. The LIC vector from our stocks uses this CMV promoter and also codes for green fluorescent protein (GFP). Thus, if the Dicty cells take in the vector by transformation and express GFP then the cells must be able to use the CMV promoter.

Transformation is the main method for inducing the expression of a protein in the Dicty cells, and is a process similar to the transformation of bacterial cells. There are two common protocols used on the Dicty cells to induce uptake of the vector. Electroporation involves exposing the cells to electrical shock which induces the cells to uptake the vector. Calcium phosphate precipitation is a form of osmotic shock that causes the uptake. Following either of transformation protocols the cells are then selected for by taking advantage of a resistance gene that is also present in the vector (Gaudet, 2007).

Depending upon the intended use of the transformed cells one method may be preferable to the other. Electroporation is recommended for experiments requiring homologous recombination. The calcium phosphate precipitation is recommended for experiments that are designed to induce an over expression of a specific protein because the precipitation results in a higher uptake of vectors per cell (Gaudet, 2007). My preliminary test requires only the detection of the GFP and could be classified as an over expression experiment. Therefore I chose to use the calcium phosphate precipitation procedure.

I have never used this protocol before and am anticipating several potential issues with the experiment. The glycerol osmotic shock must be at the correct concentration or it will lyse the cells. Along with this difficulty with the glycerol it must be applied for exactly 5 minutes or the cells will be subjected to lysis. However the large population of cells used in the protocol is likely to produce viable GFP if the promoter is used by the cells. If this procedure fails due to cellular lysis I will have to repeat the experiment and possibly remake the solutions that are used in the procedure to ensure that their concentrations are correct. If repeated failure is seen with this time sensitive procedure it may be more time and cost effective to use the electroporation method despite the lower uptake of the vector that has been observed with this protocol.

Works Cited

dictybase.org. (2010, March 4th). Retrieved January 7th, 2011, from Dictyostelium discoideum: Model System in Motion: www.dictybase.org/tutorial/

Gaudet, P. P. (2007). dictybase.org. Retrieved January 7th, 2011, from Transformation of Dictyostelium discoideum with plasmid DNA : http://www.dictybase.org/techniques/transformation/gaudet_2007_transformation.html

Reflection on “A Brief History of the Hypothesis”

The article “A Brief History of the Hypothesis” is a unique scholarly article that was published in Cell, a prominent scientific journal. This article differs from the usual topic discussed in this journal and focuses on how philosophy laid a foundation for the scientific method, specifically the hypothesis. In the preliminary sections of the article, the authors (Glass and Hall 2008), discuss the fundamental differences between a model and a hypothesis. A hypothesis is an idea or statement that is built to be subjected to falsification whereas a model is derived from data and is, in a sense, designed to be ‘verified’ by repeated experimentation. I was ecstatic to hear this distinction made. In my experience, science has been about answering questions by a method that often requires models to serve as a framework which is built upon by further experimentation.

When I think back to my years as a student in high school I realize that this was not the concept that was taught by many of the instructors. I remember writing reflections or discussing experiments and the rubric always included: “explain the meaning of the hypothesis thoroughly and accurately.” This was incredibly frustrating because often times an experiment does not necessarily need or have a conventional hypothesis; it may simply answer a question about a particular biological system or chemical reaction. This interrogative approach is often times the way that science is conducted today. Past experiences and experiments lead to new questions to try and answer.

Though Glass and Hall published this article in 2008 they present the arguments famous philosophers who have been debating the very issue for centuries. Essentially the debate centers on whether to use a deductive method of reasoning (the hypothesis) or an inductive method of reasoning (the model). Francis Bacon discredits the use of solely deductive reasoning because it confines the research to a faulty method of reasoning because the premise is predicted before the observations are made.

While Bacon and others favored a truly inductive approach, other philosophers such as David Hume and Karl Popper argued that one cannot predict future events based on the results of previous observation. To some degree this is true because there is now way to affirm that the laws of nature will always hold, but these philosophers fail to recognize the concept of probability and repeatability which serve as essential tools of data analysis. For if one could not base future decisions on actions of the past there would be no logic to perform any action over another which is truly illogical. Francis Bacon presented a solution called “true induction” where one would eliminate bias by using a bottom up approach that “confirms” or fails to disprove the proposed model.

I view this method as a combination of inductive and deductive processes that uses inductive reasoning to produce a model. This is then tested for “inductive power” (Glass and Hall 2008) by a modified use of deduction that promotes the testing of the model by a deductive approach. Glass and Hall discuss this type of application in modern medicine. Clinical trials serve as a method to accurately gain enough experience of a certain outcome so that the treatment method now applied as model can be used on other patients with the same condition. Even in this case a formal hypothesis is not necessarily needed. It would seem more logical to conduct the research by asking a series of questions that originate from prior knowledge and previous models. Thus, there are several methods by which to approach a specific problem but the most effective method seems to be using previous knowledge about the laws of nature to generate good questions that relate to the outcome of future experiments or events.

Works Cited

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