About Final movie

Naturally Obsessed: Making of the scientists

The naturally obsessed movie is focused on the life of graduate students. This video is the representation of conversion of normal people like us to the scientist.  Rob Townly is the main character of this movie who works   at the Lab of Lawrence Shapiro. Their current research is focused on the study of AMPK protein that is supposed to cause burning of fats and  obesity. So they are  are focused on protein crystallography The picture on top is  about protein purification and second on about  x-ray crystallography.

This movie depicts the life and work of graduate students. Though there several characters in this movie it shows about  the life of Rob Townley’s  and his mentor Shapiro's  success. The movie presents these two characters  as highly motivated person and determined towards research. Rob  dropped  during  under graduate , however his motivation and hard work  led him to the success..The movie ended on happy note though it showed frustration, failure and ups and downs during start.

This movie depicts the life and work of graduate students, their diligent nature. This video is  basically focused with Rob Townley’s life and his success. The movie presents him as highly motivated and detrimental  present. Earlier during his high school he dropped out thrice, however his motivation led him to the success who got  PhD at the end of movie.  The movie ended on happy note though it showed frustration, failure and ups and downs.

The movie shows that failure is the key to success. All the characters in the movie have failures in their work but they should be determined like Rob who showed his interest towards science, accomplished his work and got PhD. The failure is common for people working in the field of research. They should be able to take that as rule of nature to success. However, in the process of getting success people are naturally obsessed. They are always devoted to their work. They always think and apply as many alternatives as possible. Some are so much devoted that they forget to come out to natural world which I think is absolutely wrong. We should allocate our time to get to know the  environment outside of lab. The example of Robet can be taken as the life outside the lab work  for younger scientists  who made board and feel being climbed on the mountain . This activity is important in life because scientists are also normal people like us. They  have hobbies and interest like normal people.

The movie also demonstrates the importance of mentor.  It's utmost  necessary  that mentor should be helpful and honest . This makes sense to me because without mentor and his suggestion I won’t have achieved the J-term goal of our project, " getting best optimized transition state of Diels- Alder’s reaction". Similarly, this movie  takes about  failure which  applies to my research project as well. I ran 90-100 trials but only out  of 100   was successful in getting best optimized T.S. My own experience on  J-term is exactly similar to what movie is primarily concerned about failure. This  movie also talks about the death of Shapiro’s father. However, he was not disappointed he accepts that as normal incident. So, once we decide research as career and involve in PhD plan we need to be bold. It’s normal that some bad incidents might happen but we should be able to be stronger from any bad incident that might happen  in your life.  The film has motivated and inspired me. It energized me to pursue my career rather than discouraged by this movie.  I am confident that failure is normal  to scientists  to reach the door  of success.

References:

http://www.jic.ac.uk/staff/david-lawson/xtallog/summary.htm

http://proteincrystallography.org/

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

Reflections and Intended Career

Reflections and My career 
I pondered when I started reading the paper “The importance of Stupidity at Scientific research” and started questioning myself about how the science proven by scientific investigation is stupid.  However, I was totally agreed with him after I finished reading the whole article. The statement stupidity is an existential fact, inherent in our efforts to push our way into the unknown” (Schwartz, 2008) clarifies the importance of stupidity at research. He cited the example of his friend who drop out from graduate school and choose lawyer as his profession to elucidate its importance. The new scientific discoveries are almost impossible without being stupid. That’s why he clarified that student’ who scores good grades doesn’t mean that they can accomplish research successfully.  It’s true that science is looking for smart people but he clarified that “fascination with understanding the physical world and an emotion need to discover new things has to enter into too (Schwartz, 2008)” is important rather than grades to accomplish research as career. Similarly, as he said we are expert on our own strengthen my enthusiasm to continue research as future career.

Similarly, I pondered and started questioning on my own when I started reading the latter two articles “How to succeed in science: a concise guide for young biomedical scientists. Part I and part II I and I am  kind of lost thinking about my career. Some questions like will I be happy choosing research as career, where I will see me after 25yrs from now and so on. This article made me think at minute level. Of course I have passion towards research and I also know that research is my field but his writing made me more prepared for future.  Research needs overwhelming interest to accomplish project. In fact, his information is overwhelming to junior scientists and undergraduates willing to continue research as their profession.  The information he has given may discourage smart and dedicated students. It’s never bad to provide useful tips to get success such as choosing mentor, self-esteem yourself, choosing the program and getting advice from advisors to accomplish goal. It’s even positive to give details on these subject matters. However, he talked in-depth about PI, Postdoctoral, getting faculty position and research grants. His writing is more to frustrate iluustrating the difficulty level at concrete level which might be discouraging.  I do support his ideas that life of researcher depends on serendipity; however, it’s our responsibility to shape our serendipity. This article clicks my mind on how to place on the top of others to at this field.  On part II he suggests that teachers are responsible for introducing the techniques being involved in research. Well, this is true that beginner junior scientists need assistance from teachers. This is proved by J-term class I am currently taking where Dr. Moser help is really appreciable   to accomplish our project.  Well, I am always pessimistic about my future. These three articles has prepared me physical, mentally and emotionally. Though, I found Yewdell paper overwhelming for beginners like us but in reality it energized me.  It gave me the opportunity to get prepared from now so that I can put on top of others.  

References

http://cartoons.spuriousmonkey.com/life-of-lab-animals-cartoon-biology-or-medicine/

Schartz, Martin A. “The Importance of Stupidity in Science”. Journal of Cell Science121, 1771 2008

Yewdell, Jonathan W. "How to Succeed in Science: a Concise Guide for Young Biomedical Scientists. Part I: Taking the Plunge." Nature Reviews Molecular Cell Biology 9.5 (2008): 413-16. Print.

Yewdell, Jonathan W. "Access : How to Succeed in Science: a Concise Guide for Young Biomedical Scientists. Part II: Making Discoveries : Nature Reviews Molecular Cell Biology."

Reflection about J-term Class

J-term research for undergraduate students planning to go for graduate school is helpful in a sense that it gives them the idea of how research would be like. It helps them to figure out the problems researchers can encounter. This full time J-term research provided me the opportunity to work on research that I have not done before. My interest in research came on my mind when my friend was died from unknown disease. Then I decided to work on the field of research science. I was mentally prepared to it after I took Biology and Biochemistry class here at Loras. I learned a lot about biomolecules, protein-protein interaction and pathways that occurs in our body. I came to know that a biochemical pathway that occurs in our body is responsible for cause of several diseases. So, with a hope to know more about research and life of scientist I am taking this class which seems productive so far. 

This class has strengthened my mind choosing research as a future carrier. I have heard lot about the life of researcher. However, this research class has helped me experience and know more about their life. More from life, it is helpful in shaping my mind as research as a whole. I used to think that life as a research scientist is boring; however, this class has changed my mind. I found my project interesting in a sense that I keep on making same mistake. This develops my habit of doing only one part one day and get familiar with making protocols and keep on working unless and until you get the  desired result.  Before I start, I could think that working 8-9 hours per day would be okay. I could finish my whole project within a week. This class changed the way how I think about research and scientists in general.

The tour at University of Iowa provided me the opportunity to learn more about graduate program and the getting prepared with it. The group discussion with faculty of University of Iowa and their student was productive to me. I learned about the student selection process which is invaluable knowledge I got from the discussion. Getting to know from the official person about the program and the ways of increasing changes are important to me in my future carrier.   Experience they share with us is inspiring to me.  The lab tour was fascinating which I had never seen in my life. Biochemistry lab, NMR facility center and biology department (especially advanced microscope) are awesome instruments that I had never seen before. Overall, this tour provided an ample opportunity to getting prepared for graduate school and getting to know more about the life of the scientist.

I am positive about research and adopting life as research scientist. However, this field has certain draw backs. Research is time consuming work. It is done based on assumption and if the assumption is correct then the research is successful and he/she can move forward. Since things react differently than our prediction which is challenging task to overcome. This makes some people feel frustrated and discouraged when doing research. Even in this class I have heard most of the students chatting about their failure. This is experience I got so far is useful tool to continue my life as research scientist.

Shadowing experiment

I Shadowed Giovanni. His experiment was about nitrating toluene using a rare earth catalyst. His research dealt with the use of an environmentally friendly catalyst using specific aromatic compounds such as alkyl benzenes. The importance of this research is that replacing sulfuric acid with ytterbium triflate can have beneficial results in using less dangerous chemicals and providing minimal chemical waste to the environment. Nitrating aromatic compounds is important in the industry in creating dyes, pharmaceuticals, and other industrial products. However, Giovanni told me that while nitration of the aromatic compounds does occur, what doesn’t occur is that there seems to not be a high yield of the product. He told me that the exception was toluene. Now, he wants to test alkybenzenes and see if they might be only types of arenes that produce more of the desired product. He’ll do that by testing the electron-donating ability of toluene and cumene and conclude whether the alkyl group of the aromatic compound influences the yield in anyway; he says that the bulkier group of cumene will lead to higher yield recovery.

From my day of shadowing, I saw him separate the organic layer from the aqueous layer in the separatory funnel. He told me that the organic layer contains the desired product while the aqueous layer contains the catalyst that he used in place of sulfuric acid. He then started to add two washings of diethyl ether because it separates any remaining organic droplets still present in the aqueous layer. After the washings occurred, he showed me across his work station the rotovaporization machine. This machine serves as a vacuum suction device that dries the product so that the product can be acquired without any unwanted solution. Giovanni disconnected the flask containing the aqueous layer from the machine so that it can be reweighted and calculate how much of his catalyst was regained. He would do the same thing to the flask containing the organic layer. After the drying of the organic layer, Giovanni will weigh his flask and calculate how much of his product he has.

That was all he showed me but we did not get the opportunity for him to show me how he will identify the product. He mentioned that he will use the IR spectroscopy machine in the Organic Chemistry lab when it is properly fixed. Overall, I found my shadowing experience to be interesting. It’s interesting because we both are dealing with the underlying concept of chemistry however; I am modeling the chemical reaction while he is doing the actual lab experiment. My experiment is basically concerned with how we can model the chemical reaction.

I like his research experiment rather than mine because his research helps to develop technique for undergraduate students; however, mine is basically concerned with how to use tools to perform calculation using Gaussian program. I learned from his experiment that there are two different ways of doing experiment: one is physical where a researcher has to handle chemicals and note the change that occurs during experimentation while next one is a mathematical one where you have to deal with several theories proved by experimental procedures. I shadowed his experiment because I am familiar with Nitration reaction and its properties.

Cell theory critique

Critique on article  "A Brief History of the Hypothesis".

David J. Glass and Ned Hall described two different ideas to frame an experiment.  Two different philosophical ideas are described in their paper, “A Brief History of the Hypothesis” which are the hypothesis and the model.  The hypothesis as described in this paper is the statement of fact that can be falsified. They believe that hypothesis is always unproven because they are made prior to the experiment. However, the model as defined by them is the method developed after data is obtained from the experiment. This is based on the inductive reasoning that methods the author concludes his paper stating that hypothesis should be neglected and reference should be taken from models to predict the further result of experiment.  The author espouse that the hypothesis over thinks about the context and it’s always falsified, however, scientific investigation should always be true. I cannot support the ideas of the author and the way he justified his claims.  I believe that hypothesis is essential to guide an experiment. Scientists cannot run an experiment without any pre- planned ideas or postulates.

 The model follows the concept of inductive reasoning which states that our past results can be taken as reference to proof for future was controversial. Hume goes against this concept and gave a new concept of radical skepticism. He supported the concept of radical skepticism and goes against the concept that past experience should be used to guide the future. This concept of inductive reasoning was supported by the philosopher Karl Popper. His philosophy supported the reasoning however, he suggested methodology to solve the problem of Inductive reasoning where “concepts are subjected to falsification.” Newton even goes against the concept of hypothesis.  Newton’s ideas were that even in his creation of physical and mathematics world was based on the conclusions. If we are to follow this logic then scientists in the medical field, especially doctors and health practitioners should stop providing medicine and taking care of patients, which makes uses the concept of past experience to cure patients.

It was confusing that during early stages of renaissance period there was confusing about the use of hypothesis in scientific experimentation. The controversy on hypothesis was fueled by Galileo because his minding in mathematical world was not based on hypothesis. Even, the concept of inductive reasoning was criticized because things that happened in past was not even valid during the age of Galileo.  There was assumption that his results of falling apple form tree were based on series of data’s.

Hypothesis guides our experiment. So, I support hypothesis in scientific world though it gets falsified. In real the hypothesis is not falsified, it shows the pathway that verifies the hypothesis. Science is based on the assumptions that we can make observation and this will lead us to the reality. Science cannot prove science itself, it’s like moving in a circle that will be arguing itself. Without hypothesis the scientific method will fall apart.   

Computational Technique In predicting Diastereoselectivity

My research project for this j-term is to predict the Diastereoselectivity of (4+2) Cycloaddition addition reaction. Diels-Alder is (4+2) Cycloaddition reaction. I am testing the Diels- Alder reaction to predict Diastereoselectivity using computational modeling. We are using the computer generated program Gauss to calculate the energy of the system. The Gaussian program describes the different theories of computational chemistry that are useful in predicting several properties of a molecule like orientation, bond angle, energy of reactants and  products, vibration within molecule. It is even useful in calculating the frequency that occurs within the molecule.

Gauss program is a semi empirical method whose parameters are proved from experiment. Researchers who are working on computational chemistry can use Hartree Fork, B3LYP, MP2 and MP4 methods to predict the different properties of the molecule.  Among these B3LYP is commonly used method to predict the different structures of molecule. Along with the method it’s equally important to use basis set (describe where molecule is located) to get the reasonable result. The commonly used basic is 6-31G (d) which was proved best among others.

In my project I am using the 6-31G (d) basic set and B3LYP method to predict the Diastereoselectivity of Diels- Alder reaction.   This method is useful to characterize the transition state of the molecule.  Diels -Alder’s reaction usually contains two diastereomers. This can be done by optimization and frequency calculation.  One can use optimization followed by frequency calculation to calculate the free energy of the system. However, the Gaussian program also consists of optimization and frequency calculation at the same time which gives results about enthalpy and Gibbs free energy of the system, which helps in calculating the enthalpy of the system. Moreover, frequency calculation can predict the transition structure of the molecule.  

Any student doing research at computational chemistry especially in predicting the transition state of the molecule or predicting the diastereoselctivity of any reaction, frequency calculation should done  on a molecule on both reactants and products. The reliable method used in computational chemistry is B3LYP with basic set 6-31G (d).   So, after frequency calculation, one can calculate the bond order at transition state which is critical step to determine whether it is located at stationary points. It also conforms whether it lies within the imaginary line which confirms the selectivity by calculating the energy of both diastereomers.

Some reactions take hours to give the results even days to get desired result. So, I suggest others not to get frustration while using computational model to find results. Also, by change if anyone forget to change the basic set (describes where molecules are located), he/she can pull out the old file and can use that structure. It’s not necessary to create another structure of that molecule.

Reference:

James B.Forstman and AEleen Frisch," Exploring Chemistry with Electronic Structure Methods".