Thoughts on "Naturally Obsessed: The Making of a Scientist"

       On January 23, 2013, I had the opportunity to watch a documentary about the life of a group of graduate students called “Naturally Obsessed: The Making of a Scientist.” This hour long documentary basically talked about how graduate students lived their lives not only in the lab room, but what their personalities are like, what backgrounds they came from, and what projects they were working on. One of the most memorable individuals interviewed was Robert Townley, who started graduate school very late in his life but is very satisfied with his life choice. As I mentioned before, the audience has an opportunity to see these scientists act outside of the laboratory environment. They, just like us, have their own lives that are filled with joy, tasks, and creative hobbies (Robert built is own climbing board which recreates the effect of him crawling up a mountain while being attached to a cord). I was exposed to some techniques and projects that I have only heard but not seen, such as x-ray crystallography of proteins. (picture provided)

Cool...

 

     It was interesting to see how dedicated the individuals were with their project. For them, it was their life and some have been working on their project for years. Any type of failure is personal to them; at least that was the impression for me. One thing that I did notice was just how obsessive they were about science! In fact, there is a reason why the documentary is called like that! In order to succeed in the graduate program, they have to revolve their lives around their research. The research can be lengthy, frustrating, and life-sucking. I was surprised to see that some of the graduate students already had marriages! If you ask me, that is a bad idea since you would have to dedicate some of your life to your spouse and judging from how this documentary made grad life sound, I think it would be selfish and unfair of a person to get married while in graduate school since one actually get married to their work. It was surprising that they would show former graduate students who have left graduate school. I suppose they wanted to show how life is treating them. The woman they interviewed who left seems to be doing just fine. She mentioned that she found a good job. One thing that I forgot to mention was just how many times the documentary showed the students playing outside. I think that it was trying to show us that deep down, the grad students are people just like us and are not just a bunch of lackeys with no life except science.

                Overall, I thought the documentary was very informative in describing what graduate school would be like for anyone interested. It did a good job at highlighting the most important parts of the research process. I believe that individuals who do go into graduate schools should be people who are completely dedicated to the scientific method. Something else that I feel firmly about is also that it would be the best choice for single individuals to choose as a career. The idea of having a family and a life-dedicated research project would create too many problems, especially for your kids since you would most likely not spend more time with them. At least it would make sense financially and time-management wise to start settling down with a family after you get your PhD.  It was also a good idea of interviewing that woman who droped out of grad school. Though it may sound wrong at first, I think what the documentary was trying to say is that grad school is not for everyone and no one should feel bad about it. I give this movie 3.5/4 points of excellence!

 

 

 

References

1) http://www.naturallyobsessed.com/

2) http://videosift.com/video/Naturally-Obsessed-The-Making-of-a-Scientist

 

 

 

Stupidity in Science and Preparations for Research

I had the opportunity to read three articles written Martin A. Schwartz and Jonathan W. Yewdell, two of which were written from the latter. The articles delt with the nature of what science is, which I am fully aware of, but in a different light. In Schwartz’s short article, he mentions that it is a good idea if you “feel stupid” doing science. He did not mean that as an insult; what he meant to say was that in science, we never really know everything about nature. Through research, some of our hypotheses are shown to be wrong and our experiments may fail terribly. Often times, we can get different results that were not expected to arise from the data. These possibilities that come from the research experience can overwhelm us and we tend to feel very frustrated. Unfortunately, this frustration can lead to discouragement to continue doing research. Schwartz recounts one event in which one of his friends gave up on a science career to pursue law because she felt “stupid” in grad school. The main point that Schwartz tried to get across is that we are expected to feel as if we know nothing of our research outcomes. That is what makes research… well, research! There will be moments when we will enter into unknown territory. We will come across difficulty in trying to understand outcomes that we thought should have “never happened”. Schwartz also makes a point that during high school and college, we are used to having to do science with the guidance of a teacher. In grad school, you are all on your own, except with some advice from your mentor here and there. During grad school, it’s not just following orders in doing an experiment. We have to fully understand it and make it our own. I can relate to this feeling of “stupidity” because I did not have any previous experience with working on my own. It is also a similar in my experience in observing what my data is and how I must deal with unexpected results. For example, despite the fact that I have recreated the nitration of toluene trials from previous research, I have not obtained a yield of greater than or equal to 92%. The results upset me because it compels me to look into how I am losing so much of my product. Despite the fact that I have been trying to be careful in my techniques, I still cannot obtain a high yield. I refuse to give up in my project. These experiences prepared me for Jonathan W. Yewdell’s guide of succeeding in research.

After reading his two articles on what to do in order to succeed in research, I felt a bit overwhelmed at how many variables are involved that influence the way research is done. Granted, I am already aware of the difficulty in research that one is subjected to, but in this case a specific example was used: biomedical research. Some of the helpful tips that I read on the article made sense: the importance of choosing a good quality graduate program, choosing a good mentor, and an evaluation of what your talents and dedications are in life that will help you excel in research. He then went further into detail about how to choose your project and how to formulate your own questions. I remember when I had to figure out what to ask for the beginning of my thesis. Since I chose the thesis, my question and hypothesis have been constantly changed. With the help of my mentor, it was decided that one type of compound will be tested instead of whole wide range of compounds. Since my sample size is smaller, it is a lot easier to control. Yewdell argues that teachers should introduce students who want to go into research the basic principles being involved in it. I agree with that and to his support of it, the fact that I am taking a research class proves his point that it can be of extreme benefit to have a taste of what graduate school might be like. Reading these articles compels me to prepare heavily for a future research career in my life. It does not frustrate me and it does not discourage me to look into it. I’m glad to know that there is no shame in feeling like an idiot during research, since it is part of the scientific process. I look forward to feel stupid… in a smart way when I continue on my education. Hopefully, other individuals would take into consideration what they read in these articles so that they can know what they are getting themselves into.

 

 

References

1)      Schartz, Martin A. “The Importance of Stupidity in Science”. Journal of Cell Science 121, 1771 2008

2)      Yewdell, Jonathan W. “How to succeed in Science: a concise guide for young biomedical scientists. Part I&II”. Molecular Cell Biology 2008

Current Thoughts on Research

In this blog entry, I will talk about what my current thoughts are about the aspect of research. For the past two weeks, I have been working on my research project, which also happens to be a small part of my thesis. The entire thesis will be finished this semester before April/May. Currently, I am trying to replicate the nitration of toluene from the previous theses made about the project. The only new method that I will add will be to perform the same conditions using a different molecule: cumene. Before that, I performed five trials with toluene, which was a bit tricky to do. Some of the complications that I found were: handling the organic layer with care, buildup of pressure inside the separation funnel, and using arbitrary amounts of magnesium sulfate to dry my organic layer. More than once, I have had the unfortunate incident of accidental spills of both my organic product and my aqueous layer (which contains my catalyst that I’m trying to recycle). The first time I used magnesium sulfate, I put too much of it into the beaker containing the organic layer. That incident has made me lose much of my product and I would have much more if I used controlled amounts of Magnesium sulfate. Another problem that I had was when after I transferred my solutions after refluxing, I has to shake the separatory funnel in order to make sure that all or the organic layer was separated from the aqueous layer. This caused a built up of pressure when I used diethyl ether to wash the aqueous phase. Sometimes, the pressure would become too great that I would lose some of my liquid when the top of the funnel was in contact with it.

My general opinion of research is still positive. I still think that to do research is a fun and work-fulfilled way to discover the unknown of what nature lies in store for us. That being said, I must admit that the way I think about how research is done has somewhat changed for me. I have learned that it not always easy. Some part of my experiment were easy to do: I just had to collect a certain amount of my reactants, mix them together in a 25mL round bottom flask, and heat them up while waiting for at least 14 hours. After that, the reaction is stopped. Then the challenge arrived: getting your desired product and catalyst manually. I did not find it easy and that was the part where I learned that it is important part of research to handle my extractions with care. I often found out that research will often demand the extra mile in doing whatever it takes to minimize accidents. In my case, accidents occurred in trying to extract product and catalyst and even when I was being more careful, minor accidents still occurred and I got frustrated since I did my best to minimize mistakes. One more thing that did occur that slowed down my research was that the IR spectroscopy and rotovaporization machine could work at first or malfunctioned, respectively. I learned that when situations like this occur, I must remain patient and ask the necessary help that will assist me in repairing such malfunctions so that I may continue. In short, even though there could be roadblocks during research, it should not discourage any scientist to continue doing it. A scientist with dedication and a lot patience would be eligible to do research.

Shadowing

             My shadowing experience came from Laxman, which occurred on Thursday January 17, 2013. His experiment was dealing with a Diels-Alder reaction. For this experiment he used computational chemistry to predict the transition state of the molecule, which is a different type of method to work with desired products than what I am doing.  I use actual chemicals while he uses a computer program called Gaussian to perform the calculations.

 

 

When I arrived upstairs to where he was working, he was making the structures that he thought how the reactant, product, and transition state was oriented within a molecule. An interesting thing about his experiment is that unless the predicted structure is connecting, the calculation stops. I saw him frequently modeling the reactants, products, and transition state molecules. I even saw him with molecular modeling skit to generate ideas about how he should orient the molecules so that the specific reaction can occur. I found it fascinating when he showed me the animation of how the atoms vibrate within transition state obtained from his calculation.

          Despite the fact that I am doing an experiment procedure to my research, he is modeling a reaction. His entire experiment is basically a mathematical equation where he must know what the equation is when he already has the answer! I like his experiment because he can change the structure as many times as he wants. The software he was using has the entire feature that can add or delete any molecule.  He showed me how such tools are used to model the structure. Another interesting thing that I liked was how he was spending time on making similar models of the molecules such that the reactant, product and transition state would be oriented exactly the same way.

I liked his experiment in a sense that anyone having Gaussian software can model the structure and let the computer perform calculation. However, for my research we should be within a lab and we should follow experimental procedure. In the lab, we should be worrying about the safety measures for my research but for his research there is nothing a person has to worry about when he performs a calculation. The only concern that I thought of was that a person should be careful in saving files and pay attention to what results were obtained before the computer goes on to the next equation/model to work on.

            It feels to me that there is underlying concept of physics on his research which is very tough to understand since I had a lot of difficulty in that class. I imagine that anyone with a strong background in physics and math would have an easier time to understand just how and what the equation should be. One more thing that I would like to add: I chose him to shadow because it dealt with Diels-Alder reactions, my second favorite reaction. It also dealt with a type of chemistry that I was not familiar with: that of math and computation. It was remarkable that a computer did all the work for Laxman. In my case, it would have taken me a long time to do the reactions by hand.

 

Thoughts on "A Brief History of the Hypothesis"

I was given an article to read this week written by David J. Glass and Ned Hall. This four page long paper explains the philosophical implications of the hypothesis. It is argued that there are two frameworks: the hypothesis and the model. The hypothesis is “an idea or postulate that must be phrased as a statement of fact, so that it can be subjected to falsification instead of verification”. However, the model has no use of the hypothesis, since it is an unproven assumption that can taint our perception and results that make up reality. The model is based off of inductive reasoning, which allows the scientist to conclude that the past results will yield exactly the same ones in the future.

                It came to my surprise that there seems to be a controversy about the existence of a hypothesis in the scientific method. Newton apparently did not use the hypothesis for his observations of how the physical world works.  It is also interesting that the idea that past results of observations will yield to same results in the future is criticized. Scottish philosopher David Hume rejected the idea that our past events predict the future. One reason that I can think he would conclude that has to be that we must assume that in order for us to use inductive reasoning, everything from previous conditions will be the same. An apple falling from the tree and landing on the ground may not land in the same place tomorrow. This is best described as the “problem of induction”. The article goes further into depth by mentioning Critical Rationalism, a philosophy created by Karl Popper who tried to follow in the footsteps of Hume’s radical skepticism.

                Despite all of this, the use of inductive reasoning had been defended from the criticism it has received, especially from the medical field. If doctors were to follow this logic, then they would not be able to give more medicine to their patients because past treatment would not allow the patient to become healthier. The main conclusion of the article is that we should abandon the hypothesis and allow the use of the model.

I have to admit that the article was a bit condensed to read and a bit confusing. The idea of the hypothesis being considered to be discarded is something new to me. Even if it is an unproven assumption, it does not make it false. Science operates under assumptions that can’t be proven, either! To say that “we will use science to prove science” would be arguing in a circle! It has been my experience that the hypotheses is based on what has been observed and make a prediction. Falsification is an important concept of the scientific method. Even if the hypothesis cannot be verified, it does not make it false or biased against reality. The use of the hypothesis is one of the first steps in understanding how a naturalistic phenomenon occurs.  I like the idea of a model but I find it to be empty without a hypothesis because it lacks authoritative strength in a statement that relates to the hypothesis. I think David Hume goes too far in his skepticism for past and future observations. From firsthand experience, it can be shown that, under the right conditions, past events can be recreated.  I say that the hypothesis should be kept.

REFERENCES

1) Glass, David J. & Hall, Ned. "A Brief History of the Hypothesis". Cell. 134, August 8, 2008.

A Technique in Nitration of Toluene using Ytterbium Triflate

This is my first post pertaining to my thesis. I am exploring the use of rare earth metals for the nitration of aromatic compounds. Previous research has shown that the use of lanthanides have environmental superiority over sulfuric acid (1). The use of corrosive acid is reduced, which greatly benefits the health of the environment. The question, however, about is economic use is still unanswered. In this specific project, I will attempt to recreate previous conditions that led to the creation of higher yields in toluene only. The last time this project was done, the reaction, while successful in nitrating activated arenes, did not yield high amounts of the product, the exception being toluene (2). A particular question that must be answered is whether this greener method of nitrating can only yield large amounts of the desired nitrated product when the substrate is an alkylbenzene? The reasoning as to why alkylbenzenes are the only activated arenes that nitrate successfully AND produce a high yield is caused by the electron donating nature of the alkyl group of toluene toward the ring. My hypothesis is that the bulkier alkyl group of cumene will have a higher yield than toluene.

 

Classical Nitration

 

Sulfuric acid is generally fond in the classical nitration method. The reaction begins with an aromatic compound reacting with an electrophile, such as the nitronium ion that is derived from nitric acid.The formation of the nitronium ion begins when nitric acid deprotonates sulfuric acid, which eventually forms water, sulfate anion, and the nitronium. The substitution of the nitronium ion into the aromatic ring forms two different isomers of nitrotoluene: ortho and para. In Green Chemistry Nitration of toluene, the lanthanide ytterbium triflate is the ideal environmental and economic method of obtaining nitrated aromatic products.

A Specific Technique Performed in my Project

I am being asked to describe a technique that I am doing for my research. One technique that I have done is the refluxing of my reactants.  I set up a reflux apparatus by obtaining a heating mantle, a condenser, and a 25 mL round bottom flask. After they were put together, I added my reagents according to optimum condition concentrations. This is important because under these conditions, I can maximize the amount of product created after the reaction. The temperature during reflux should be at a moderate level; just enough for there to be some boiling. Tubing should connect to the condenser and water should be flowing though so that the high temperature from the heating mantle does not evaporate the product. The length of the boiling is to be at least 14 hours. Refluxing at short time periods can cause the product to not be produced at high levels. It is imperative that all of the toluene be nitrated. Longer reflux time allows this to happen. The reaction is to be quenched with water, which will cause the reaction to cease. There should be two layers: the aqueous and organic layer. These layers will be separated with the help of a separatory funnel and undergo rotovaporization  in order to dry the catalyst and the product. The yields will then be calculated.

 

References

1) Braddock, C. Green Chemistry. 2001, 3, 26-32

2)Whitcomb, Tyler J. Using Recyclable Nitration Catalyst as an Environmental and Economical Alternative for the Nitration of Activated Aromatic Rings May 2009

 

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