Naturally Obsessed Reflections

Today in class we watched Naturally Obsessed: the Making of a Scientist.  This movie follows Dr. Lawrence Shapiro and a group of his graduate students Rob, Gabe, and Kil.  This research group’s task it to try to create a module of the AMPK protein using larger protein crystals.  Through years of research, Rob finally made a breakthrough and successfully modeled the protein, landing him in Science Magazine and earning him his doctorate.  Gabe eventually pursued another science career in Chicago and Kil eventually earned his PhD.

Picture found at
 http://oxford.bside.com/2010/films/naturallyobsessed_oxford2010

            Although the movie itself was very informative in the AMPK proteins, the stress was placed on the emotions and struggles these scientists as well as others go through by choosing a research career.  It took this group of individual’s years of repeated failures to finally find a protein crystal they were looking for.  The sheer mystery behind this research is expressed when other scientists were trying pickle juice in their experiment.  One must almost go into the lab knowing you are going to fail to be able to do the same repeated steps with no idea of what may be the problem, run your trial, and get nothing back.  As the movie is titled, you would almost have to be ‘naturally obsessed’ to have the drive to continue to do this type of research.  And not every scientist has this obsession.  Gabe proves this by dropping out of her graduate class to pursue other goals.  And who can blame her really?  The salary that these researchers made was only $24,000 a year.  Here that is not much, but in New York that is next to nothing.  And because you don’t know when you will finally earn the coveted doctorate, you have no idea when or even if you will ever improve your salary.  And like what they said in the movie, they could quit right now and pursue another science career that makes upwards of $100-200,000.  What makes them stay?  Kil said it’s the urge or the passion to find the answers to a question you have worked so hard to achieve.  Kil and his fiancé even parted ways because of the amount of focus and determination that Kil needed in this career.  As our professor stated, this is not the norm in research in that researchers go years into their studies without a single success.  Nevertheless, reading from How to Succeed in Science: A Concise Guide for Young Biomedical Scientists there is very little room in a researcher’s life.  The paper stated that only one other love can co-exist with research and not much more.

            Comparing my research to that of the research in the movie had similarities and differences.  One of the interesting things is that I recognized many of the instruments the scientists were using with only a few weeks of lab experience.  I took a small My work also deals with proteins.  However, my research as of now is on such a small scale compared to the work that they were trying to do.  The work they were doing took years (hopefully mine does not) with results that could alter how we fight obesity and diabetes.  I also didn’t have the absolute success or failures that these researchers shared.  I had my first gel fail and my Dicty cells did not want to move the first time I recorded their movement.  However, I had recent success in keeping the Dicty cells motile and happy and recorded some pretty neat videos.  And hopefully I will get a successful gel tomorrow.  In my opinion, it would take more courage and perseverance than brains when it comes to research of that magnitude and length.

Works cited

Rifkind, R (Producer). (2009). Natural obsessed: the making of a scientist [Television series episode]. (Executive producer), New York:   ParnassusWorks.

Tewdell, JW. How to succeed in science: a concise guide for young biomedical scientists. Nat      Rev Mol Cell Biol. 2008 May;9(5):413-6.

How is this for becoming engulfed in your own research!

Hey guys,

I remembered seeing this video on 20/20 about the brains of killers.  Check it out!

http://www.youtube.com/watch?v=cnV4RnWcmWo

(In case you didn’t want to watch it and to take my word for it)

Dr. Fallon is a researcher and professor who studies the human mind.  More specifically, he studies the brains of violent criminals.  Through his work, he has found a pattern in the minds of killers of little activity in the orbital cortex.  This part of the brain is responsible for morality and behavior.  To prove his study, he was sent seventy MRIs from various doctors that had a mix of killer brains and 'normal' brains.  When he analyzed the MRI’s, he pointed out the five killers of the seventy scans.  He then came to the conclusion that aggression and immoral behavior is inherited through the “warrior gene” that is passed down from mother to daughter.  Here is where the story takes an almost Hollywood twist.  When he was given a book about his family, it showed a line of murders.  This included seven murders throughout his family line, including his early grandfather killing his mother and his cousin who killed her father and step-mother with an axe.  Intrigued, he scanned his family member’s brains and it turned out he had the mind of a killer!  His orbital cortex was showing no activity, just like all the other serial killers and psychopaths he had been studying before.  He then tries to figure out why he was not a killer himself.  He finally placed the reasoning on his upbringing.  He said that his family nurtured and loved him.  He believes that this kind of living environment was the major factor into whether he was going to be an inspiring researcher or a killer.

            This article brought up a lot of questions in my mind.  First was the social usage of Dr. Fallon’s findings about the correlation between orbital cortex activity and the possibility of future violence.  I am unsure of at what age this can be detected, but if it can be found at an early age in a child’s life, should we as a society put forth money towards scanning children’s brains to keep an eye out for the ‘potential killers’?  Dr. Fallon has already shown that these can be easily identified.  Would the cost of finding these matches and teaching the parents how to properly raise their child be worth having fewer violent acts in today’s world?
            Another question that Dr. Fallon brought up is the power of free will in violent acts in people.  He believes that a serial killer is bred and without nurturing can almost be fated to become a killer.  With these new ideas about the human mind, should we as a society change the ways in which we punish criminals (ex. mentally insane receive treatment instead of time behind bars or executed)?

Let me know what you think!

Evaluating Science in the Popular Media Assignment

The article I have chosen for my science in the popular media evaluation comes from CBSnews.com.  The article is titled Statins Sometimes Raise Stroke Risk, Study Says: Who’s at Risk?  From an average readers perspective this is an important article concerning those who have had or at risk of having a stroke.  Statins such as Lipitor, Zocor, and Crestor are drugs used to lower bad cholesterol.  Since bad cholesterol is often associated with strokes, many patients who have had strokes have taken statins to lower their cholesterol in the hopes of preventing another stroke.  However, Dr. M Brandon Westover believes that doctors should use caution in giving a statin to people who have had bleeding in the brain due to a stroke.  Doctors who researched these findings stated that statins might prevent clotting in the brain if another stroke occurs in a patient.  These findings are supported by Dr. Larry Goldstein who accompanied the study.  The paper states that, “In the absence of new data to the contrary, statins should generally be considered off-limits to these patients.

            Looking at this article, a reader may take the assumption right away that statins are drugs that should be avoided if they have already had a stroke.  The work was done by a respectable Massachusetts General Hospital Doctor with the support of a prestige Duke University doctor. One of the doctors even came to the conclusion that, “doctors shouldn’t prescribe statins to people who have suffered an intracerebral hemorrhage.”  The work is also published in the May issue of “Archives of Neurology”, a respectable journal.  They also point out what they think is the reasoning behind the dangers of statin usage.  From an average reader, this must be a pretty conclusive article about the dangers of statin use in post-stroke patients.

            On the other hand, there are many flaws in this article to validate it from a scientific perspective.  When looking at a science article, one must look at the methods of how the research was conducted.  In other words, how did these doctors come up with this conclusion that statin use is dangerous for patients who have had a stroke?  To be honest, there is little if any methods expressed in this article.  The only statement that this article made concerning how this research was conducted was that, “He (Dr. Westover) said the computer model at the core of his research suggested that whether statins make sense may depend on the location of the intracerebral hemorrhage.  Absolutely no data or even layman numbers were given in this article.  The questions that a scientist could ask about this research article are close to endless:  What software was used in this model?  How was this research conducted on this software?  What was the size of your sample?  What were the sample’s age, gender, and overall health?  How were these samples chosen?  Were there any controls or placebos?  Was there any sort of hypothesis or prediction leading into this experiment?  At what dosage were the statins given?  How often were the statins given?  Some if not most of these questions need to be answered to make a complete assessment of this research.  The questions of sample size and diversity of the sample are needed to validate this experiment to see if the researchers ran enough trails and if they did not test a certain group of people such as age.  More precise questions such as the usage of a control/placebo or hypothesis asked the question of if there were other factors involved in the usage of statin or not, including possible bias from the doctors.  This bias could go as far as if these doctors have a personal view against these drugs (a less obvious question, but a question to ask none the less).  There is also no counter argument against this statement or citation of any other work done in this field of research to support the doctor’s claim.  Overall I believe that this article was good at giving bold statements, but lacked the substance of how they arrived at those answers to validate these statements.

            I believe that the information given in this article is exaggerated.  Looking back, the base case for the computer analyses was a 65-year-old male intracerebral hemorrhage survivor.  I believe that a large diverse sample would yield more confident results than one older male.  They then based their results on quality-adjusted life expectancy in which they projected how many more years their patient would live if they took statins and if they did not take statins.  Most of the projections supported the fact that not taking statins did increase the life expectancy to around 2-2.5 years in outer brain hemorrhaging.  However, when they tested hemorrhaging deep in the brain, taking statins only shortened a projected lifespan of 0.8 years.  Even in the comments section, the authors discussed the limitations of their work, including only using a single clinical trial and only using an all-or-none strategy in which they did not mix some statin use along with other therapies in patients.  Although this research paper does include results against the use of statins, I believe other tests of other designs are needed before the media writes a report on the evils of this drug on stroke patients.  I believe that this story was slightly exaggerated due to the writer either putting too much faith into this one article’s truthfulness, or the need to write a paper worthy to be put onto CBSnews.com.  After all, it is there job to write a paper in which people will want to read (biasness at work here?)

            So what should we do to validate or reject the notion that statins are unsafe in patients who have suffered from a stroke?  This question is quite difficult due to the nature of this experiment.  The obvious experimental design would be to gather a large and diverse sample of patients who have already suffered an intracerebral hemorrhage.  Because the article and the research states that there statins may have different effects depending upon the location of the hemorrhage, the sample should include as many different hemorrhage areas as possible.  Then, you can run a double blind experiment and give one section of the sample a statin, either specifically using one of the major statins (Lipitor, Zocor, and Crestor) or all three.  The other group is given a placebo.  Then observe the short and long term effects of the statins to see if the data shows any significant difference in the amount of second strokes between the two groups.

            Now I may not have taken an ethics course, but I do understand the underlying problem that this method might kill our patients, something we as researchers are not out to accomplish.  Other possible ideas are to run trials on lab rats (how you would get them to have a stroke in this first place is beyond my knowledge).  You could also study and research the actual drug itself.  A researcher could break down the components of the drug to see its possible effects on the body, especially its anti-clotting abilities that could prevent clotting in a intracerbral hemorrhage.  Another possible area of research is to test the effects of certain statins in small amounts along with other procedures to reduce the risk of high cholesterol and another stroke.  Restated, more tests (and different designs of tests) are needed to either validate or reject this notion that statins should be entirely avoided in patients with stroke histories.

Literature Cited

Freeman, D (Writer). (2011,January,11). Statins sometimes raise stroke     risk,  study says: who's at risk [Television series episode]. In    (Executive producer), CBSnews.com. CBS. http://www.cbsnews.com/8301      504763_162-20028116 10391704.html

Westover, B, Bianchi, M, Echman, M, & Greenberg, S. (2011). Statin u     following intracerebral hemorrhage. Archives of Neurology,    Retrieved   from  http://archneur.ama        assn.org/cgi/content/full/archneurol.2010.356

Overview of Research and How to Handle Being Stupid: Article Reflections

Over the weekend, we were assigned to read three articles.  These three articles were How to Succeed in Science: a Concise Guide for Young Biomedical Scientists Part I: Taking the Plunge and Part II: Making Discoveries by Jonathan W. Yewdell and The Importance of Stupidity in Scientific Research by Martin A. Schwartz.  Although combined at nine pages in length, the papers were very easy to read and gave insight on what it means to be a researcher, how to be a successful researcher, and my personal favorite, dealing with ignorance in research (O how I can relate).  All of these articles gave very good points involving research and can also be related to my future career goals in the health field.

          Part I in How to Succeed in Science: A Concise Guide for Young Biomedical Scientists was all about becoming a researcher or as the title called it: Taking the Plunge.  In this article, Jonathan outlines scientific research in the United States today.  He starts off his paper in an unusual way: by describing the depressing news that very few people striving for researching doctorates will ever become an independent researcher, and that those who do will spend most of their time and energy searching for grants to perform their experiments.  With this woeful future in store, Jonathan then reminds us of the importance of science, in that we as a society need advances in science to advance our own species.  He then breaks down the specifics on what it takes to be a happy and successful researcher.  And although I do not plan on taking a strict researching career, many of the tips Jonathan gives to researchers can be used in any career field.  A main area of concern involving graduate work is choosing the right institution and mentor.  By breaking down the different types of PIs to the criteria one should use in picking a mentor, one can relate these to any other field.  From picking the right hospital to choosing the right boss, who you work for not only influences your personal happiness, but you future endeavors as well.  And as of right now, I believe that I chose the right institution for my future in our school’s Science Department professors.  I believe they can give the tools needed to succeed in my future science career.

          Another major factor that Jonathan includes in Part I of his paper is the work ethic needed to be a successful researcher.  He breaks down the number of hours one should spend on science and that these hours should not be considered work.  Again, this can easily be applied to not only a career but life as well.  Whether it is medical school or marriage, I know that life takes work.  It requires as Jonathan stated, “a major commitment of your body and soul”.  And we have to enjoy it if we plan to end our lives with a smile on our faces.  Although the workload is plentiful, the rewards in putting forth the effort in research and life as well are well worth it.

          In part II of Jonathan’s article, Making Discoveries, he breaks down the crucial components of running an experiment.  He reflects on the designs of the experiment, the size and number of tests needed, how to properly write in a lab notebook, how to look at the smallest of details to get the right results, and the reasoning to go on your own paths of discovery.  Although at my point in researching I am a far cry from going on my own, I am slowly starting to grasp these other points.  I am learning how to use my notebook to jot down EVERYTHING I observe and to move away from the way I used to write up my lab notebook in O-Chem. with step by step procedures.  I am also learning that running one significant trial is not enough, and that many failed as well as successful tests need to be done to validate my findings.  Such is the case in my recordings of Dicty cell movement, in which I try to get as many videos in as possible to add credibility to my work.  This article also gave some insight in how to keep a lab room happy, including shying away from lab romances (sorry Ty L), and learning to deal with criticism (which is not always the easiest to do).  He finishes with a basic comment concerning research and life as well: Be sure to have fun with it!

          The final article which happens to be my personal favorite was The Importance of Stupidity in Scientific Research.  This one had to be read to understand its meaning.  No this article was not implying that a person can do research with very little brains.  This article begins with the fact that a co-researcher quit researching due to the fact that it made her feel stupid: the fact that a person may not know what is going on in their research.  He then touches base on the fundamental difference in research compared to scientific studies in a classroom: I liked science classes because I was good at knowing the answers.  This gave me a feeling of accomplishment and joy.  In a scientific research standpoint, we know longer know the answers and must now enjoy the ride of finding those answers!  I learned quickly that I know longer know the answers in this class.  As researchers, we need to embrace the fact that we don’t know what may be going on, but do the best of our ability to find the answer.  The second we lose this notion is the second we begin to frustrate over why we are wrong.  I leave you with my favorite line, “One of the beautiful things about science is that it allows us to bumble along, getting it wrong time after time, and feel perfectly fine as long as we learn something each time.”

Articles Read

Schwartz, MA. The importance of stupidity in scientific research. J Cell Sci. 2008      Jun 1;121(Pt 11):1771.

Yewdell, JW.  How to succeed in science: a concise guide for young biomedical scientists. Nat Rev Mol Cell Biol. 2008 May;9(5):413-6.

Should All Scientific Findings Be Published?

Hey Guys,

            I found this interesting article on the web:

http://news.yahoo.com/s/ap/us_sci_haunted_scientist

            In this article, Dr. David Nicholas works with chemicals to figure out how the brain works.  Using these results, Dr. Nicholas then publishes his work to science journals in the hopes that others can use his research to find cures for brain diseases such as depression.  However, Dr. Nicholas has a unique problem that raises ethical questions involving public display of research results.  Some of his chemical concoctions are being used on the street to make illegal drugs.  Dr. Nicholas himself says he knows five of his chemicals have turned into illegal drugs that have killed some of the drug abusers.  Dr. Nicholas discusses his haunting of indirectly killing someone and raises the question of should all scientific works be published for all to see?  Dr. Roland Griffiths believes that the way we advance as a scientific community is through the free exchange of findings and ideas.  However, Dr. Art Caplan believes that there are certain circumstances in which research should not be published to protect society from using it in the wrong way.

            I talked this over with Brennan, and he brought up another good point about this problem: If a researcher does not publish his work, he is at a severe disadvantage when it comes to gaining grant money.  So I leave you with a question, “Should all scientific findings be published for all to see?”  Leave your comments on about the question, the article, or alternatives you can think of below.  Thanks!

Research Reflection

I knew three months ago as the fall semester drew to a close that I would need to take a J-term this year to get my first one ‘out of the way’.  However, I did not find very many classes to my liking.  I looked at classes such as Positive Psychology and even Go Dog Go.  I then found Forensic Science and decided to give it a go.  As I was walking out, I noticed our Professor had a class; Intensive Science Research Experience.  The very name of the class did not sound appealing at all.  Looking through the brochure made it even worse: class from 8:30 to 4:30, a 300 level class, only three credits!  Then the question was what I would study.  I had no idea of what I would be researching. 

“Is there any more room in that dog class your taking?” I asked my friend.

“Nope, but you have fun with your science class!” he snickered back.

            With no idea of what I was getting into, I decided to sit down with our professor to pick her brain about her class.  She told me that the students were to pick mentors in the building to work with them in their research.  I decided to go with our professor in her research on Dicty cell movement concerning PCH proteins (with an extremely minor factor that she was also the only professor with room for another researcher).  Right away I found it interesting.  It almost felt surreal thinking about how I could be toying with another organisms DNA, along with the fact I was going to try to make them glow! (Kind of Frankenstein-ish in a way).  After getting a little bit more background, I decided to pull out of Forensic Science and go with the Intensive Science Research Experience as my J-term class.

            With the weeks leading up to J-term, I was still nervous about how the class was going to go.  I had visions of sitting in a lab for eight straight hours trying to get something to work, forced to stay later if something did not go right.  O the endless amounts of researching, writing papers, and dealing with our professor who will probably be breathing down our necks! (Ok, maybe an exaggeration, but you get the point).  This was going to be a long three weeks.  How could someone enjoy doing this for their entire lives?  At least it would look good on my resume.

            My stereotypical notions of what researching went out the door the very first day of class.  Although it was true that compared to now I had very little knowledge in my research or how research was conducted, I struck an immediate interest in conducting research.  It was awesome to think that I was actually designing primers for my DNA.  Although it was a tedious process to figure out the DNA sequences of primers, the day flew by in my newfound excitement of what I was doing in the lab.  The next few days went by even faster, with learning about new machines, how they worked, culturing my first plate of dicty cells (ahhh….it seemed like only yesterday), and making SM media.  It was neat to think that all the scientists in the world started out just like me.  Although it was a bit frustrating at times having to take things slower and asking questions all the time, the wait was well worth it, as I now am gaining more independence in my research, although my mentor is still needed immensely.

            These last two weeks completely changed what I thought of research and what it would mean to be a scientist for a career.  I no longer think of it as a lonely, isolated job with a ball and chain attached to you and your research.  It is true that a lot of the work is very drawn out and does require a couple extra hours in the lab.  But researching with others in the same field is such a neat experience.  I can ask questions and bounce ideas off others, research my topic online, make solutions, use the microscope, and even record videos.  Right now with everything so new, it feels like I’m adding another page to my repertoire of researching techniques every day.  And above all, it’s actually fun and exciting to see how your results of your hard work turn out (although frustrating at times).  Through these last two weeks, I’ve come to understand why so many people take the path of researcher in their careers.  You have a sense of pride and importance in your work, because it is usually something completely new that no one has ever done before.  The one stereotype that was ingrained even more was the passion that some scientists can develop for their research.

            Looking back, I am glad I chose to take this course and do research over J-term.  It has shown research and science in a whole new light.  It has answered the questions of why people devote their entire lives to it.  I have taken such a liking to it that I plan to continue it during the spring and even summer semester if I can get away with. I leave you with a quote my friend and I had over lunch one day.

“Hey, what did you do in your dog class?”

“Not much really, had to sit through a lecture for three hours, then I had to socialize with some dogs, how about you?”

“O not much really, just figured out primers to use in my DNA, grew some of my dicty cells, and even got a video of them migrating.  It is actually some pretty neat stuff.”

“Wow, I really think YOU got the fun class.”

Shadowing Experience

On Wednesday, January 13th, I shadowed Ryan O. In his research, he is trying to convert different vegetable oils into usable biodiesel. With a better understanding of his background into the subject, I was better off understanding the similarities and differences we had in our separate experiments.
I asked Ryan a few questions on the background of his research. From his explanation and his Powerpoint on Friday, Ryan is trying to convert various oils (olive, vegetable, among others) into biodiesel using enzymes. He explained that to convert oils into biodiesel, you need some sort of catalyst. Two examples of catalysts in the conversion of biodiesel are enzymes and acid/base reactions. Since his mentor Dr. Maslowsky is already involved in converting oils into biodiesel with acid/base reactions, Ryan decided to take the other catalyst and use enzymes in his reaction. I asked what the purpose of his experiment was since scientists have already discovered ways to convert vegetable oils into biodiesel. He answered that although there are ways to convert vegetable oils into biodiesel, tweaking different chemicals, amounts, and procedures in the process could alter the biodiesel yield in his final product.
Leading up to today, Ryan tried to create biodiesel out of certain oils using 95% and absolute ethanol. With little luck in producing a significant amount of biodiesel, Ryan decided today to use methanol. He explained that the alcohols were used in the reaction to combine with the oils to exchange esters, leading up to

Process of converting oil into Biodiesel
http://utahbiodieselsupply.com/gettingstarted.php

 biodiesel. What he was working on at that moment was trying to immobilize his enzyme. From previous knowledge, Ryan knew that immobilizing an enzyme before using it in a reaction speeds up the reaction and would hopefully produce more biodiesel in his experiment. To immobilize the enzymes, Ryan dissolved his porcine enzyme powder in a phosphate buffer and combined that with Celite. He then placed the flask containing this solution into liquid nitrogen, flash freezing the solution. Ryan also believed that it might have sublimed as well. He then hooked up his flask to a vacuum filtration system and tried to separate the water crystals from the liquid enzymes to the best of his ability. While the solution was being vacuumed off, Ryan already had one product that was ready to be tested using the Infrared Spectroscopy. Looking at the results, Ryan found next to no biodiesel and a significant amount of water in his product. He thought that this may be due to the oil surrounding the water molecules and preventing them from evaporating out of his biodiesel product.
Comparing my experience with Ryan’s research and my own, we have a lot of similarities and differences. One thing with both shared is that we both had unforeseen speed bumps in our experiment. In his, he was working with the IR machine instead of the NMR. He was also using a vacuum filtration system that looked like a machine used in Thomas Edison’s time. He explained that as with the NMR, the newer and better vacuum was not working. He explained that this less efficient vacuum may poise consequences in his results. I also had issues, particularly my cells. With my first video, I used too much light with the microscope. This caused the Dicty cells to ball up instead of move towards the food gradient. We also shared mundane and drawn out procedures in our experiments. For Ryan, it was simply the time needed for his reactions to take place. He said that he would sometimes have to let some of his solutions sit out for days to get the water out of them. He also said the hours needed to incubate his solutions were a time consuming process.
The drawn out part in my experiment is the care needed to keep my cells alive. I need to make sure that they are not overcrowded on their dishes. So every day or two, I have to wash the Petri-dishes, pull the cells off, count how many cells there are, figure the concentration of cells needed, and then finally re-plate the cells.
We also have some unique differences in our research experiences. One of them is the amount of time the mentor is with us. I asked how much time Dr. Maslowsky is with him while he does the experiment. He said not very often, since Dr. Maslowsky has his own J-term. He said he’ll discuss problems or ideas, but for the most part he is solo in his experiments. This lone ranger approach is the opposite in my research. With Dr. Cooper heading this class as well as constantly running through the DNA lab helping other students, I can always find her and ask her question about my research, what procedures I should use, and what the significance of certain steps. Another difference is the research differences. The reason I chose to work with Ryan instead of Ty or even Kara, is that Ryan had chemistry as his central science in his research. I also had some chemistry in my research as well, but mine is predominantly a biological research experience. It was quite a difference going from strict cleanliness requirements to using only chemicals in your experiments.
I am glad I chose to shadow Ryan for my assignment this week. Ryan’s research gave me a break from the DNA lab and let me into a different form of research that was solely based in chemistry. It was also interesting to know that the biodiesel he is making is used in everyday life. Shadowing a fellow researcher definitely gave me an insight into another’s work, and broadened my conception of what research was all about.