Well, it's official, I am now a Ph.D. candidate! It means I get to move on and continue my graduate school career. See, getting a Ph.D. is not like getting your bachelor's degree, where pretty much all you have to do is pass your classes and you get your diploma. Sometime in your second year, you have to write and present two proposals, one on your own work and where you want to go with it, and one outside your field of study. These proposals are presented to a committee of professors who are experts in the field you choose. Their job: rip your guts out and show them to you. Or at least, that's what it felt like.
Really what they're there to do is take apart your proposal and challenge you to defend it. If you handle yourself well, show that you've read a lot of background info, understand their criticisms, you get to pass, as long as there are no major problems with what you've done. Unfortunately, I had some problems. I forgot that there is a right way to ask questions in science, and a wrong way, and I did what every new scientist does and approached it the wrong way. The first thing my committee did was to point this out and re-frame my question the way it should have been asked. Then, they proceeded to point out that most of the experiments I had proposed were irrelevant to this new question. Furthermore, I had based my proposal on contradictory results from two different labs doing similar work. My committee thought it was an interesting subject, but had a quick and easy answer, one that I apparently should have seen as well.
Needless to say, I came out of this feeling pretty awful. It's never fun feeling like a stupid amateur, and it left me wondering if I even belong here in the first place. But, I don't feel that any of the criticism I received was unjustified or off the mark. It's just difficult looking at yourself through the eyes of four people who have years and years of experience and seeing all your flaws laid bare. I've felt pretty awful for the last two days, but really that's what makes it such a valuable learning experience. These are mistakes I'm not bound to make again. And I did pass the exam, on the condition that I re-write part of my proposal. Having gone through this is just going to make it that much sweeter when I finally do get that degree.
Sunday, May 8, 2011
Monday, April 25, 2011
Bugs and guts: Dr. Judith Eisen explains how the nerves in the zebrafish gut affect the bacteria that live there
*Note: One of the assignments for my Science Journalism class is to keep a blog, although strangely enough it doesn't have to be an actual blog, just a word document that has all the things we would blog about. Anyway, I have't posted here in a long time (been busy), so Jen suggested I just post my assignments. Here's the first one I wrote, hopefully it's interesting enough. I'll most likely post the others as they get written.
Of all the cells in your body, only about 10% percent belong to you.
Kind of gives you a new perspective on things, doesn't it? According to Dr. Judith Eisen, a researcher at the Institute of Neuroscience at the University of Oregon, the other 90% is made up of a conglomeration of bacteria and other microorganisms. Most of these microscopic hitchhikers are beneficial to us, which is one reason our body doesn't fight them off, and many of them live in our guts. In her laboratory at the U of O, Dr. Eisen and her team study how the nervous system another vertebrate––the tiny zebrafish––affect the population of microbes that live there.
Normally we envision bacteria and other "germs" as being detrimental to our well being, so it seems odd to think that innervation in the gut affects the microbes, and not the other way around. But this is exactly what researchers in Dr. Eisen's lab have found. During a genetic screen, a process by which animals with interesting defects are generated by randomly mutating their DNA, members of her lab found a zebrafish mutant that lacked pigment cells. Upon closer inspection, they found that it also lacked nerve cells in its intestine. The lack of nerves causes the muscles in the intestines to fire randomly, or not at all; this is in contrast to normal intestinal muscle, which have controlled rhythmic movements.
Examination of the microbes living in the gut of these mutant fish revealed that there were many types not found in normal fish. Eisen’s team hypothesized that the movement of the intestinal muscles helps move the microbes into their proper position. In order to test this, they set up a simple experiment using two different types of bacterial "food". The movement of the food through the intestine can easily be monitored, thanks to the fact that zebrafish are transparent. Normal “wild” zebrafish were initially fed green bacteria, and its movement was monitored over a stretch of several days. Then, the fish were switched to red food. Over time, it was possible to see the green food disappear, replaced by the red food. In the mutant fish, however, all of the food was trapped at the entrance to the intestine. This data helped prove that their hypothesis was correct.
The reason Dr. Eisen's lab has chosen this area of research is that it is directly applicable to human health. One disease in particular, Hirschsprung's disease, is caused by a lack of nerve cells in the intestine. The mutant zebrafish studied in her lab is a good model system in which we can study and understand this deadly affliction. Furthermore, Dr. Eisen stated in her presentation that many neurological diseases have a related gastrointestinal (GI) component. At this time, it is difficult to determine if the GI problems cause the disease, or the other way around. Hopefully, the work done by researchers like Dr. Eisen will help to clear up this conundrum.
Of all the cells in your body, only about 10% percent belong to you.
Kind of gives you a new perspective on things, doesn't it? According to Dr. Judith Eisen, a researcher at the Institute of Neuroscience at the University of Oregon, the other 90% is made up of a conglomeration of bacteria and other microorganisms. Most of these microscopic hitchhikers are beneficial to us, which is one reason our body doesn't fight them off, and many of them live in our guts. In her laboratory at the U of O, Dr. Eisen and her team study how the nervous system another vertebrate––the tiny zebrafish––affect the population of microbes that live there.
Normally we envision bacteria and other "germs" as being detrimental to our well being, so it seems odd to think that innervation in the gut affects the microbes, and not the other way around. But this is exactly what researchers in Dr. Eisen's lab have found. During a genetic screen, a process by which animals with interesting defects are generated by randomly mutating their DNA, members of her lab found a zebrafish mutant that lacked pigment cells. Upon closer inspection, they found that it also lacked nerve cells in its intestine. The lack of nerves causes the muscles in the intestines to fire randomly, or not at all; this is in contrast to normal intestinal muscle, which have controlled rhythmic movements.
Examination of the microbes living in the gut of these mutant fish revealed that there were many types not found in normal fish. Eisen’s team hypothesized that the movement of the intestinal muscles helps move the microbes into their proper position. In order to test this, they set up a simple experiment using two different types of bacterial "food". The movement of the food through the intestine can easily be monitored, thanks to the fact that zebrafish are transparent. Normal “wild” zebrafish were initially fed green bacteria, and its movement was monitored over a stretch of several days. Then, the fish were switched to red food. Over time, it was possible to see the green food disappear, replaced by the red food. In the mutant fish, however, all of the food was trapped at the entrance to the intestine. This data helped prove that their hypothesis was correct.
The reason Dr. Eisen's lab has chosen this area of research is that it is directly applicable to human health. One disease in particular, Hirschsprung's disease, is caused by a lack of nerve cells in the intestine. The mutant zebrafish studied in her lab is a good model system in which we can study and understand this deadly affliction. Furthermore, Dr. Eisen stated in her presentation that many neurological diseases have a related gastrointestinal (GI) component. At this time, it is difficult to determine if the GI problems cause the disease, or the other way around. Hopefully, the work done by researchers like Dr. Eisen will help to clear up this conundrum.
Friday, January 7, 2011
Learning to Walk
So, normally I'm against New Year's resolutions. I've always thought that if there's something in your life you want to change, then change it. Why wait for a holiday that really has no significance to decide to start being a better person (whatever that means)? But I've recently decided to make a change in my life, and my decision just happens to coincide with New Year, so I guess I really do have a New Year's resolution this time around. I've decided that I need to learn how to walk.
Now obviously I can walk, in a literal sense; I mean it metaphorically. I've been blessed with the ability to learn things quickly, which allows me to become pretty good at most things without too much effort. I'm not claiming to be a master at everything, and there are some things that I'm just plain bad at, but for the most part I can perform at an above-average level at most tasks. Because of this, I've gotten in the habit of trying to do too much too soon. For example, not too long ago I had my first meeting with my advisory committee, the purpose of which was to explain to them what work I'm currently doing and where I'll be going in the future. One of the techniques we use is sort of specific to worms, so I knew I needed to go into a little more detail when describing it. I made this really complex powerpoint slide with tons of animation for my talk, and it looked great. I was (and am) proud of it. But I got over-confident. I was thinking "Okay, I've got this really good slide to explain the most complicated part of my talk, and all the rest of this is just stuff I do everyday, so it should be easy!" I didn't even practice my talk before I gave it; hell, I didn't even finish it until an hour or so beforehand. But because I had done so well on that one part of it, I was convinced it was going to be a home run.
It wasn't.
In fact, I kind of made an ass of myself in front of my committee. Afterward I felt pretty humiliated, not because my talk didn't go well, but because I know I'm capable of more, and I just didn't even try. And I've found myself doing it again. I've always had an interest in martial arts. I've read several books on various types of martial arts, I'm familiar with the various strategies and philosophies of many different styles. When I watch a UFC match, I try and relate what I've read to what I'm seeing, and try to figure out what I would do in different situations. But I've never actually had much hands-on experience with martial arts. I just recently joined an MMA gym to try and change this, and once again I'm trying to run before I can walk. Instead of taking my time and really getting the most out of each drill, I'm busy trying to just "be good" at everything by relying on my conceptual knowledge. But it doesn't work, and I can tell you from experience, getting punched in the face is a really good, quick reminder of that.
So that is my new goal: learning to walk. I'm going to learn to take my time and really focus on building a good foundation before I move on to more challenging and difficult tasks. Unfortunately the problem with learning is that you have to screw up a few times before you can get it right, and I really don't like making mistakes (especially when they result in pain). But what's life without a few bumps and bruises?
Now obviously I can walk, in a literal sense; I mean it metaphorically. I've been blessed with the ability to learn things quickly, which allows me to become pretty good at most things without too much effort. I'm not claiming to be a master at everything, and there are some things that I'm just plain bad at, but for the most part I can perform at an above-average level at most tasks. Because of this, I've gotten in the habit of trying to do too much too soon. For example, not too long ago I had my first meeting with my advisory committee, the purpose of which was to explain to them what work I'm currently doing and where I'll be going in the future. One of the techniques we use is sort of specific to worms, so I knew I needed to go into a little more detail when describing it. I made this really complex powerpoint slide with tons of animation for my talk, and it looked great. I was (and am) proud of it. But I got over-confident. I was thinking "Okay, I've got this really good slide to explain the most complicated part of my talk, and all the rest of this is just stuff I do everyday, so it should be easy!" I didn't even practice my talk before I gave it; hell, I didn't even finish it until an hour or so beforehand. But because I had done so well on that one part of it, I was convinced it was going to be a home run.
It wasn't.
In fact, I kind of made an ass of myself in front of my committee. Afterward I felt pretty humiliated, not because my talk didn't go well, but because I know I'm capable of more, and I just didn't even try. And I've found myself doing it again. I've always had an interest in martial arts. I've read several books on various types of martial arts, I'm familiar with the various strategies and philosophies of many different styles. When I watch a UFC match, I try and relate what I've read to what I'm seeing, and try to figure out what I would do in different situations. But I've never actually had much hands-on experience with martial arts. I just recently joined an MMA gym to try and change this, and once again I'm trying to run before I can walk. Instead of taking my time and really getting the most out of each drill, I'm busy trying to just "be good" at everything by relying on my conceptual knowledge. But it doesn't work, and I can tell you from experience, getting punched in the face is a really good, quick reminder of that.
So that is my new goal: learning to walk. I'm going to learn to take my time and really focus on building a good foundation before I move on to more challenging and difficult tasks. Unfortunately the problem with learning is that you have to screw up a few times before you can get it right, and I really don't like making mistakes (especially when they result in pain). But what's life without a few bumps and bruises?
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