"Naturally Obsessed: The Making of a Scientist"

The movie Naturally Obsessed: The Making of a Scientist seemed to bring together everything we have already discussed/observed during class as well as bringing in a slightly new perspective. We have already discussed “productive stupidity” and observed people working in the lab. When we visited the University of Iowa Biochemistry Labs and at lunch with a few professors and graduate students, we learned that working in a lab is hard work, although most of us probably could have told you that from experience. This was especially evident in the movie and I think that the title describes it well. A person basically needs to be obsessed with learning new things and working until he or she finds an answer. The only way one can get to this point is by asking questions, working to solve those questions, and then asking more questions. Without questions, scientists would not have made the progress they have and we won’t continue to make progress. This sense of being obsessed with asking questions and trying to answer them is an aspect I hadn’t really considered before seeing the video. I knew that researchers often spend a lot of time in the lab, but I had never really thought of it as being obsessed, but I think that obsessed is probably the best word that could be used to describe it.

The video gave me even more things to think about as far as doing research as a career. They asked some of the people in the video why they did research and their answers were the typical “it’s interesting,” and “I want to answer questions.” While these are probably my typical go-to answers as well, I think that I will probably need to spend some time really thinking about this question and trying to find my real motivation. As of right now I think that these two answers along with wanting to help others are my main motivators.

Another topic that the video spent a lot of time on was the idea of successes and failures. They made the observation that one often has countless failures before just one success. I have found this to be true in my own research. I have found that learning to accept failure is one of the hardest things for me to do. Because this is so hard for me to do, I really liked how the video pointed out that the difference between success and failure is actually quite small. One may try many of the same things in both successful and failed projects. The successful one just means that you did everything in the correct order. Even though one may fail many times before he or she is successful, it only takes one success to have a breakthrough. This is why one should never give up. That one more experiment could be the one that works. This is still a work in progress for me, but I’m sure it’s something I’ll get used to, especially if I decide to pursue research as a career.

In addition to working on accepting and learning from failure, should I pursue a career in research, I will need to learn how to work more independently. I know that I’m still just a beginner as far as research goes and it’s acceptable for me to ask for guidance from my research mentor and lab partner. They have both told me that they would rather I ask questions, even if it’s just to clarify something, than to proceed without asking and be uncertain. I believe that asking these questions allows one to build confidence in the lab which in turn leads to independence. The people in the video said that they felt much more independent once they got to graduate school and that it was something that took a little bit of time to get used to. They said that they had to learn how to not rely on their advisor so much.  While I’m still not entirely confident or independent in the lab, I feel as though taking this J-term class has helped a lot in those areas. I used to be scared to do anything in the lab without either my lab partner or mentor available for questions, but now there are some things that I am confident in doing completely on my own. Again, this is something that will come with time, but I was reassured by the people in the video and the fact that they said it took them time before they were completely comfortable being independent in the lab.

Overall, I’d think that this movie gave me just a little more insight into what a career in research might be like as well as more things to think about. I’ve definitely enjoyed this J-term, but I think I have a lot of things to consider and think about before I make a final career choice. It’s a good thing I have a little bit of time before I have to make that decision. I’m hoping to continue my research here at Loras as well as apply for several summer research programs next summer, if not this summer. In the meantime, I’ll continue to live in the science hall and be productively stupid.

Stupidity in Science...Do you have what it takes?

As a part of our class we were asked to read the articles “The Importance of Stupidity in Scientific Research” by M.A. Schwartz and “How to Succeed in Science: A Concise Guide for Young Biomedical Scientists” by J.S. Yewdell. I will admit that I was actually quite excited about reading these articles, even if it was mostly because the titles sounded interesting. I mean, how often does an article make stupidity sound like a good thing? I thought that the length of the articles were perfect for busy college students and the information was wonderful, at least for someone who is interested in doing research as a career. I will do my best to summarize the articles and give my thoughts in less than 1000 words, so if you really want to know what I’m talking about, check out the articles.

The title “The Importance of Stupidity in Scientific Research” really drew me in. I was mostly interested in seeing how they defined stupidity because scientists and researchers are often thought of as “super smart” or “geniuses.” This article went on to describe how students often like science in high school and college (undergraduate) because they are “good” at it. In other words, they often score well on tests, which makes them feel smart. I would say that in high school I was “good” at science. I took as many science-related classes as I could and thoroughly enjoyed almost all of them. When I started taking classes at Loras, I still enjoyed them, but not as much as I had in high school because they were harder. I actually had to study in order to learn the material. I do remember telling some of my friends that my classes made me “feel stupid.” After reading this article, I’m realizing that these feelings are okay. In fact, it mentions that I will need to get used to the feeling if I’m going to pursue a career in research. There is a lot of information in the science world and we don’t have to know and understand all of it. It helps to have at least a basic understanding of a lot of different principles, but the feeling of “stupidity” that we encounter can actually be quite helpful. It can help us to ask questions, both of ourselves, our research, and of others. This sense of “stupidity” is what helps us to keep moving forward in the science world. The article is not suggesting that we don’t try to learn, but that we choose to ask questions and investigate despite knowing what we already do. It mentions the idea that in research, we cannot even be sure if we’re asking the right questions. I invite you to ponder the following passage along with me: “Productive stupidity means being ignorant by choice. Focusing on important questions puts us in the awkward position of being ignorant. 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” (Schwartz). Do you have what it takes to be “productively stupid?” I’d like to think that I have what it takes, but I think only time will tell.

I found the second article just as thought-provoking as the first. This one was entitled “How to Succeed in Science: A Concise Guide for Young Biomedical Scientists.” As I mentioned in a previous post, I would like to have a career doing medical research, so I felt as though this article was giving me advice for the future. The first section of the article describes the perks of science, graduate school (including finding a school, program, lab, and mentor), the emphasis on skills rather than just published works, what it takes to have a career in research, and a post-doctoral work. While I’m not at the point of choosing a graduate school/program or a lab, it was still useful information. Even at the undergraduate level if one is going to do research (or even if one doesn’t want to do research), I feel as though having a good mentor or advisor is extremely helpful. The article outlines a little bit of criteria for finding such a person. I think that my mentor fits the description. J Although I’ve only been doing research for a little over a semester, I can see how the things mentioned in the article, especially about the mentor will be very important in a research career. The second part of the article describes choosing a project, as well as designing, performing, and interpreting experiments. This is still valuable information, but it doesn’t seem quite as useful right now. Should I end up in a career involving research, this will be even more useful.

Although I am still trying to figure out what I would like to do in life, I think it is good for me to read things like these articles. They give me a chance to imagine myself in a research position. Many of the qualities and attitudes that were described seemed as though they were describing me and I can definitely see myself in a position where I am developing and running my own experiments. Although I know that my path won’t be easy and it will take hard work and dedication to reach my goal of being a medical researcher, but I think this article puts it best: “[I] will never have to worry about running out of things to discover.”

 

"The Importance of Stupidity in Science"

"How to Succeed in Science: A Concise Guide for Young Biomedical Scientists" (part 1)

"How to Succeed in Science: A Concise Guide for Young Biomedical Scientists" (part 2)

Experiment Shadowing

For my experiment shadowing, I followed Matt Sanford in his work on the “Antibacterial effects of glucosinolates produced by Garlic Mustard (Alliaria petiolata).”

Today I observed Matt plating two different strains of bacteria. Each of his plates was separated into three sections (the cover of his plate was divided, not the actual gel) and is used to test a chemical, positive control, and negative control. He uses the Kirby-Bauer disc diffusion method to treat each area of the plate. After the plates are left at room temperature for 24 hours and he observes bacteria growth, he measures the zone of inhibition. He uses this data to observe the effects of each different chemical, control, or concentration. From what I understand, he does this same thing pretty much every day in order to practice his technique and collect data.

He mentioned a couple of things that could potentially be problems with his project. The first being that the discs for the antibiotics come pre-soaked with the antibiotic and the other discs must have the liquid placed on them. He controls for this by making sure that the rest of his method stays the same. Another thing that he mentioned was measuring the zone of inhibition. Because the standard method for measuring the zone of inhibition is done with a ruler and is subject to one’s own opinion, there is room for bias. He gave the example of rounding down for a control and rounding up for an experimental zone, if he knew that the control was supposed to be smaller than the experimental. To control for this, he said that one could have someone else who does not know which zone is which do the measuring. This would allow for one to be unbiased in his or her measuring.

His project seems very different than the one I’m working on. One of the biggest differences that I observed is the fact that he wants to repeat his experiment many times in order to gather data which will then be used to draw conclusions, whereas in my project I don’t necessarily want to repeat my experiments. There are some parts that I would want to repeat in order to confirm findings, but for the most part I want to be successful in my different experiments so that I can move forward to other experiments.

Although our projects are very different, there are a few similiarities. One of the biggest similarities that I found was that both projects are extremely tedious, but in different ways. For Matt’s project he has to do things such as sterilize the tweezers, put a small amount of liquid on a disk, and then place that disk onto his plate. In my project I am often working with small amounts of liquid, placing liquid into very small wells, and observing things under microscopes. We also both work with some of the same equipment such as pipettes and we’ve both plated  bacteria as part of our projects.

I’m the kind of person that gets bored easily, which is why I’m thinking about doing research as a career. Depending on what one is working on, research can be ever-changing which would help keep my interest and turn into a career that I love. In the research that I’m working on, I do something different or new pretty much every day. I may have to go back and repeat a trial or a technique, but I usually have a couple of other steps to do in between which means that I’m not doing the exact same thing every day. In other words, I found it interesting to be able to shadow another student and learn what their research was about, but I think I’ll stick with my own project for now.

Is a career in research for me? (and a little bit of randomness)

Many kids go through a stage where they ask the question “why?” after everything. My mom likes to say that I never grew out of that stage and as much as I hate to admit it, I think she’s right. I’m definitely not as obnoxious about asking why as I used to be, but asking why and then trying to find the answer and understand is an important part of research.

While I would like to keep a research aspect in my career, I would also like to be able to help others. This too, has always been a part of my life beginning when I was very young. The combination of these two aspects is why I’m leaning toward medical research. I would like to be able to improve treatments or find a cure for diseases or conditions. By doing this I could potentially help many people.

I went into this J-term thinking that I would like to do medical research as a career. I’m trying to figure out what medical research actually means or what I might want to study specifically, but I can see research in my future. Now that we’re a little over a week into the three-week class, I have found the idea of doing research as a career more appealing. There is just something about it that draws me in. Don’t ask me what that something is, because I haven’t quite figured that out yet, but when I do I’ll let you know. I have found out that the days can be long and exhausting, but they can also be very rewarding.

I’ve found a couple of down sides with doing research as a career. One downfall that I’ve discovered during J-term is the lack of schedule. I’m someone who likes to know what’s going on ahead of time and that’s hard to do when what you do is based on how things from the previous day turn out. I’m pretty sure that I could learn to deal with this, especially if I was doing my own research and planning my own projects. A second downfall I’ve found is the amount of public speaking. There are few things that I dislike more than speaking in front of other people. As we heard from some of the people we met when we traveled to Iowa City, sometimes this fear of public speaking goes away with practice and other times people just learn to deal with it. Because I can’t tell the future, I can’t say which one would be true for me should I go into research as a career. There is also the possibility that I can do research without having to present my findings. A third downfall is the lack of interaction with other people. Although I’m an introvert, I’m not sure that I would want to work alone. During J-term, I’ve basically been working with one, sometimes two, other people, but once in a while I would like to work with more people. The amount of people I work with would depend on where I was working and what I was doing. Obviously there will be downsides to any career, but one can find ways to either deal with those downsides or find more positives that outweigh the negatives.

Although I’ve found downfall with research as a career, I can still definitely see myself doing it and J-term has confirmed that. It has shown me what it would be like to work full time in a lab doing research. Although this is what I think I want to do as a career, change is always a possibility.

My ultimate goal would be to work with clinical trials. In working with clinical trials, I would hopefully be able to have patient contact as well as be in the lab researching to see what works and what doesn’t work. For me, this would give me the best of both worlds. I’m not exactly sure what area I would like to work in, but as of right now my top choices would be cancer research or something to do with neuroscience. In working with clinical trials, I would be able to interact with people as well as do the research that I love. I would hopefully be able to see my work in action.

One of the best things about having a career in research or science in general is all of the fun that can be had. After a peer and I finished a project involving liquid nitrogen, our mentor gave us the bucket and told us to “go have fun.” Now, this was my first experience with liquid nitrogen, so I had no idea what to do with it other than pour it on the ground like she had showed us. We asked our professor what we could do with it and he suggested freezing a rubber tube and then breaking it, so that’s what we did. At first we tried to break it “wishbone style” but were unsuccessful, so we decided to use a hammer instead. Who would have thought that you could shatter a rubber hose? After that we had a little fun pouring it onto the benches and watching the little beads dance and scatter before disappearing almost as quickly as they had appeared. We ended up sending what we had left down the hallway. We essentially sent the little beads down the hallway in a race to see how far the beads would make it before they disappeared. My guess is that they probably went 25 or 30 feet.  We all need a little scientific stress relief once in a while. Come on, you have to admit it, science is fun!

Breaking the rubber hose after it had been frozen in the liquid nitrogen. It ended up shattering all over the lab which resulted in slightly more clean-up time than we were expecting, but it was fun nonetheless. :) 

Here's a short video of us pouring the liquid nitrogen onto one of the lab benches. The little beads that you can see are what we sent down the hallway. Who wouldn't like to do something like this? 

Hypothesis?

Hypothesis. It’s a word that seems to be thrown around in science classrooms everywhere, but do you know what it really means? What if I told you that it’s meaning changes depending on the scientific method viewpoint you’re using? Even dictionary.com has several different definitions and I’m going to list them here.

1. a proposition, or set of propositions, set forth as an explanation for the occurrence of some specified group of phenomena, either asserted merely as a provisional conjecture to guide investigation (working hypothesis) or accepted as highly probable in the light of established facts.

2. a proposition assumed as a premise in an argument.

3. the antecedent of a conditional proposition.

4. a mere assumption or guess.

While these explanations make sense, they aren’t necessarily true or the way some people, especially some scientists would use the word. I had to rethink my idea of what a hypothesis was after reading the article “A Brief History of the Hypothesis” by David J. Glass and Ned Hall and having a class discussion about it.

Personally, I found the article, “A Brief History of the Hypothesis” to be very interesting. I had never really given much thought to the fact that we often use the same word, but give it different meanings based on the context that it’s used in. I think that most people outside of the science discipline believe that a hypothesis is simply a prediction about an experiment, but I’m learning that the word “hypothesis” is quite ambiguous. In one context, a hypothesis may mean a prediction, but in another model, a hypothesis might be replaced by a question.

                During the class discussion, I found the comparisons of the different scientific methods fascinating. The way I understand it, one model of the scientific method starts with an observation (or possibly a law) which leads to a hypothesis (or a model) which then leads to an experiment. The experiment can lead back to an observation, leaving one with a circular pattern. If an experiment has the same results repeatedly, a theory may be written. Until this theory is proven, it will remain a theory. This model of the scientific method uses the language of model rather than hypothesis and believes that the use of the word “hypothesis” is actually distorting it’s meaning. This model recognizes the feedback loop that is used to gather as much information as necessary for a complete understanding. People that use this model often describe the “hypothesis” as a model or question, make predictions, and use inductive reasoning. It seems to me as though this is the model most often used by scientists because the predictions can be modified which is not the case with the second model.

In the second scientific method (the mathematical model), the hypothesis is a statement that must be falsifiable. The hypothesis can lead to postulates. This method uses deductive reasoning and does not have a feedback loop. This system has a very cut and dry way of deciding if something is valid or not: If the postulate is valid, the hypothesis is valid. While this may seem simpler than the other method, it could also create many more problems. It doesn’t leave room for modification. If the hypothesis is invalid, one must start over.

After looking at and comparing the two models/definitions for hypotheses, I can definitely see why members of the scientific community use the model they do and don’t even typically use the word hypothesis. To be honest, I think that using the word hypothesis just makes things more confusing rather than clarifying them.

On a side note, I’d like to comment on the mention of philosophy in this article. I used to think that philosophy and science were two completely different topics, but after reading this article, I see how philosophy may have influenced science. I realize that many philosophers reject the idea of inductive reasoning, but I still think that science and philosophy could be related (or maybe I’m just interested in both and am trying to put the two together). I particularly liked the part about whether a chair is still the same chair if it is left in a room alone. The philosopher argued that one could not be sure that it is the same chair because there was no one there to observe it. Hume says that one cannot predict future happenings based on past experiences. While I agree that one cannot prove that something will be the same because of past occurrences, I disagree in saying that one cannot predict what will happen. One can make a prediction, but they cannot prove anything. I’ve learned that we do not prove anything in science, we can only disprove things. From my understanding, it seems as though philosophy does basically the same thing, if they even go so far as to actually disprove things.  Has science been influenced by philosophy? Has philosophy been influenced by science? Will they influence each other in the future? I will leave you to ponder these questions, but I hypothesize… or rather, predict that there is and always will be an interaction between the two.

Gel Electrophoresis

A technique that I have used several times both in research and my biology classes is gel electrophoresis[1]. Gel electrophoresis can be used to separate DNA, RNA and proteins by length. An agarose gel is made up of agarose, 1x TAE (Tris-acetate-EDTA), and Ethidium Bromide. It is then poured into a tray that is placed in a holder that has sides that hold the agarose in the tray until it has hardened. A comb is also placed in the gel in order to create wells for loading samples. The agarose gel that is used as a separation medium has a web-like structure which allows smaller particles to pass through more easily than larger particles. This gel is then placed in a small tank and covered in a solution containing salts. This solution conducts electricity which carries the molecules through the gel. Samples are then loaded into the gel using a pipette. Because the samples are colorless, they are mixed with a dye before being loaded into the gel. This makes loading easier and allows one to see the movement of the samples. A ladder is also loaded along with the samples.

The tank that the gel is placed in has a positive pole and a negative pole. DNA has an overall negative charge because of the negatively charged oxygen found in the phosphate groups in the backbone of the DNA. Because the DNA has a negative charge, it moves toward the positive pole of the tank when the electrophoresis unit is turned on.

After a specified amount of time, the electrophoresis machine is turned off and the gel can be looked at using ultraviolet light. A small amount of Ethidium Bromide is added to the agarose gel. The Ethidium Bromide attaches to the DNA and then glows when exposed to UV light. This allows one to see where the DNA ends up after running the electrophoresis. The location of the bands can then be analyzed by comparing them to “markers” that are found in the ladder. These “markers” are segments of DNA of known sizes.

In doing this technique several times there are a few things that I’ve learned or have been told are important. When loading the gel I usually rest my elbows on the table and hold the pipette with both hands. I then place the pipette tip just above the well, taking care not to put the tip too far into the well (this could cause holes and the sample to spill), and insert the sample. I’ve learned that this takes practice and I’m still learning. The gel is very slippery and will easily come off the try if it isn’t held onto. When lifting the tray out of the tank, I usually grip it in a way that allows me to have fingers on both ends to prevent the gel from sliding off. I have also learned that the gel can be wrapped in plastic wrap and stored in the fridge for another use if there are still available wells.

The following are things that I always double (or sometimes even triple) check:

·         What I’m adding to the sample. Make sure it’s dye and not ladder.

·         That the lid is placed correctly. The black cord/end of the lid is placed on the black end of the tank and the red cord/end of the lid is placed on the red end of the tank.

·         Make a note of what was placed in each lane.

·         Always run to red! This means that the wells must be placed at the black end of the tank.

·         The time. One must be careful not to let the machine run too long because samples can run off the edge of the gel, ruining all of the work that one already put into a project.

Here's a picture of a gel after it's been run through the gel electrophoresis machine.

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[1] "Gel Electrophoresis" Biology Animation Library :: DNA Learning Center. (n.d.). DNA Learning Center. Retrieved January 9, 2013, from http://www.dnalc.org/resources/animations.