Duke University | Howard Hughes Undergraduate Program

Howdy,

So today I’ll give you a little more specifics about my actual research project. As I said earlier, if memory serves me right, I am experimenting to test whether a certain genotype of drosophila melanogaster have preferences in the substrate they lay eggs in. I am particularly focusing on sugars. This is important because on the theoretical level because it delves into the neuroeconomics of drosophila. Since each drosophila female’s primary goal is to increase her genetic fitness, she has a propensity to lay eggs. However, eggs are a limited commodity, that take time and resources to produce, so the opportunity cost of laying an egg somewhere is the ability to lay an egg elsewhere, which might be a better spot. Since drosophila are fruit flies after all, we are using sugar concentrations that they might expect to find in fruit; grapes, in particular. On the more practical level, this could show if fruit flies have preferences for certain fruits at certain times of development based on their sugar concentrations.

My starting hypothesis is that the flies will prefer sugars found in fruits that are ripe as opposed to those that are unripe and in the process of ripening. As fruits ripen, sucrose is converted to glucose and fructose, so unripe fruits have high concentrations of sucrose while ripe fruits have high concentrations of glucose and fructose. I hypothesized that the flies might be able to distinguish between the sugars and have different egg laying behavior, because it might be expected that the sugars on the ripe fruit would be more advantageous and the fly would develop an evolutionary attraction to those sugars. It was unclear whether there was any specific inhibition in sugars found in ripe fruits; although it is possible that flies could have evolved a response to prevent them from laying eggs on unripe fruit if enough ripe fruit or similarly beneficial substrates were available that there would be a better substrate than the unripe fruit. Wow that was a mouthful. But would the flies really be averted from laying eggs by a sugar? This is something I hope to know in a month.

Another thing I have really taken in so far is the amount of things you have to control in the experiment. In an orgo lab class, you are given a specific protocol for your experiment. However, in the real world, you have to design all of the parts of the experiment. This is different from course labs in that all of the materials you need aren’t conveniently located in your beaker. You often have to creatively design materials for the protocol you are using. This is the case in the plates we made. We originally made plates that were way to large for our design, and the drosophila did not lay many eggs. What we want to do is essentially see how they react with a basic choice; so it makes more sense to give them a small area that presents them with that choice and leaves less room for error. With an animal such as drosophila that you have to raise, many factors can come into play that can effect its behavior. These are critically important, because, when you are testing for a single variable such as sugar type/concentration, you have to be careful you’re results aren’t from any of the other details of the experimental set-up. One thing we’ve changed from our experimental set-up was the time the flies were subjected to the sugars. We originally designed the experiment so the females would have two hours to make decisions, but we found they were not laying enough eggs. 24 hours seems like a more reasonable amount of time for the type of data we are trying to collect.

If we have enough time, we might test some of these other variables to see whether they make a difference in the decision making of the fruit fly. These can include the length and number of females and males mated, the type of agar substrate we use as a medium between the two sugar substrates, and type of food we provide the flies with in the deprivation stage (which we might also consider eliminating in a few trials) after mating.

So that is my basic project, so far. And my preliminary results? You’ll have to keep tuning in. =) Right now we are still in a slow period because the new bottles of flies from the genotype I am using are just about ready for the two-hour mating and 24-hour deprivation steps, which we need to do before we run the actual experiment.

In other news, unfortunately Elliot Williams is transferring from Duke, and will no longer be a part of our men’s basketball team. With Gerald Henderson leaving early for the NBA draft (tomorrow night I believe), some of the other guys are really going to have to step up. We cannot lose to Carolina twice again this year!

Later,
Nick
 

It’s probably not proper science to hope for something. It would be much better to simply get it right. But, as a human being, it’s kind of natural to hope for certain things, whether we expect they will occur or not. Going along with this, I feel like it will really make my summer feel more meaningful if my hypothesis turns out to be right. One could argue this hope is mainly for egotistical reasons—to provide me with personal reassurance. And, of course, as the saying goes, it journey is more important than the destination. To a certain extent, I can’t really control what the results are in my lab, as it is up to the natural world to provide me with truth and results. However, what I can control is the methods I use and the work I do. So perhaps, this should be my focus. To learn as much as possible and perform my experiments with the expertise of a graduate student.

On the other hand, no one really sets goals based on their effort. Usually, goals based on results can be just as effective, because to get to the desired point, you must go along the particular path anyway. So, what I hope to be able to show is that the drosophila will prefer the substrate mimicking the ripe grape over the unripe grape. I think this will be awesome because, as it was taught to us in different terminology I can’t remember at the moment in Writing 20, I will be effectively continuing the conversation. It is like responding to someone by saying half “wow, that’s such a great idea I want to work on it too,” and half “nice try, but this is how (I think) it really works.” Okay, at least in my case, it’s probably mostly the former. But if everyone was right about everything there would be nothing to research. And I don’t think we’ve hit that point in any major fields. Anyway though, I hope to have a substantial result that I can feel proud of at the end of July. Hopefully, I will be able to get results on some of my basics experiments fairly soon, so I can play around with some other variables I have in mind that might even make for more interesting results.

Additionally, I expect I will be able to tell virgin drosophila apart from non-virgins by the end of July. I think I have pretty much mastered the male-female dichotomy. However, identifying virgins is more of an acquired skill, if you will, as it takes a bit more practice and feel, because older virgins are much more similar to non-virgins. The line is a little less blurry between males and females, in which drosophila tend to be one or the other. The trick to easily finding virgins is to do it quickly and often before they lose their virginity. From what I understand, pupae that turn into flies usually take about 8 hours or so before they start mating, so usually the second and third checks of the day will turn up mostly virgins.

Also, one of the lab’s graduate students, Richard, successfully defended his thesis today. He gave a presentation that summarized a lot of his research. I was amazed at the clarity of his presentation. I think they must secretly give public speaking courses in graduate school, because I marvel at how well professors and people with Ph.D.'s speak. He started his presentation by defining “pain,” and went all the way up to the boundaries of what he has done and what there is yet to discover. And yet he did it in a manner that someone who basically knows nothing about drosophila (i.e. me) and someone who knows seemingly all there is to know about drosophila (Dr. Tracey, although I’m sure he won’t admit this) could understand and be engaged in the lecture. Well, I admit, I couldn’t keep up with a lot of the terminology and genetics, but I still felt like I understood, to some extent, what he has done in his time at the lab.

After the presentation, he got grilled by a committee of faculty of members for an hour. I didn’t see this but I’m assuming he did really well because there was a party afterwards. One of the most useful things I have learned so far at Duke is to take advantage of free things, most notably T-Shirts and food. The reception had some great cheese, brownies, and sandwiches. It just means less cooking for me.

Actually, I haven’t done any cooking here yet. It’s the result of bringing a car and being too close to a Chipotle and the wonderful restaurants of Durham. Durham doesn’t get enough credit for its dining. Everywhere I have been to in this city is good. Still, the realities of being a college student are starting to set in, so my roommate, Arun, and I decided to load up at the local Target. A word of advice: don’t shop at Target when you are hungry.

In other news, I highly recommend none of you watch the movie Mega Shark vs. Giant Octopus. Although the name alone sets a tough standard, the movie succeeds in being every bit as much of a joke. Without giving too much away, basically there is a giant shark, a giant octopus (not a squid, mind you), and a bunch of environmentalists freaking out. This movie does absolutely nothing to dispel many of the false stereotypes of scientists often portrayed in the media. The scientists are shown as nerdy and socially awkward, and disconnected from the rest of the world. The movie also has hilarious scenes in which I’m pretty sure the directors put just about every flavor of Kool-Aid in viles. It apparently takes the “scientists” a long time of mixing the blue and yellow liquids (which turn green, no less) and the like to realize their chemistry isn’t working. And lo and behold, they find an apparent solution in a place they were not expecting it. This relates to something Dr. Tracey mentioned a couple times when I interviewed him the past week. Much of modern academic science is based off the competition to get limited grants, which can often be fierce and discourage collaboration among scientists. While hard-core capitalism might suggest this competition is a good thing because it prompts the researchers to do the best work (note for clarification that I am inserting my own views now), often there is a fight for grant money and an emphasis on proposing projects that test hypothesis that have more immediate consequences as they might get approved more easily. There could be a lot more freedom given to scientists and researchers. Basically, from what I’ve seen first-hand, no one is in academic science primarily for the money, so there isn’t a lot of greed (compared to the financial industry, which seems saturated with greed). It seems then that it would make sense to put a lot of money in scientists hands and give them more academic freedom.

The other problem I had with the movie was that the scientists wore clean white lab coats while doing all of their experiments, but seemingly did not even think of putting on gloves or safety goggles. Because this is Hollywood though, they were fortunate enough to have a better ending than the infamous Carol.

Unfortunately the Wings couldn’t come through, thanks to a last minute crossbar-rattling shock and some shaky officiating. At least Wimbledon’s going to be starting in a week.

Nick
 

Hey,

My name is Nick Schwartz.  I am from Ann Arbor, Michigan, where it is not 90 and muggy every day in the summer. Actually, I haven't really had any problems with the weather here so far.  Maybe that is because I have been in the lab during the hottest part of the day though.  But I have found it quite nice at Duke, so long as I properly hydrate.

So, on to the meat of the post: my lab. I am working in the lab of Dr. Dan Tracey.  The Tracey lab studies drosophila melanogaster, more commonly known as fruit flies. Drosophila is a useful organism because many mutations have caused there to be different genotypes that are easily distinguishable and it has a relatively short life cycle, making it useful for genetic research. Since other organisms, such as humans, possess many of the same genes as drosophila melanogaster, understanding the genetics of fruit fly can go along way to understanding other biological life. For reasons such as this, its entire genome has been sequenced.

Dr. Tracey’s lab focuses on pain signaling and nociception in drosophila, but I am doing my project on something slightly different. I hope to study the decision making of drosophila feeding on different sugars. It has been found that the sugar sucrose can actually inhibit drosophila from laying egg. At first glance, this does not seem to make a whole lot of sense because drosophila are attracted to high sugar substances to feed and lay eggs. What we hope to do is perform a lot of tests with a variety of sugars to find any basic preferences. Then, we are planning on trying to mimic the concentrations of sugars in grapes, and see what sense we can make of drosophila’s apparent inhibitory response to sucrose. There are also some other variables we can manipulate depending on our findings. Hopefully, this will allow us to understand the decision-making mechanisms of drosophila better. As the summer progresses, I’ll post more on how my research project is coming.

One of the first things that comes to mind, well, for me at least, when someone mentions research, is people manipulating complicated machinery and obtaining results that only a specialist would be able to understand. However, this is not the basis of research. To quote Polonius completely out of context, “Though this be madness, yet there is method in it.” One thing that has stayed fairly constant in Western Science over the past couple hundred years is a reliance on the Scientific Method, and I don’t see that changing anytime soon. It turns out collegiate laboratories are no different from seventh grade science projects in this regard. Dr. Tracey places a lot of emphasis on creating a hypothesis before you do start experimenting around with the flies. This makes a lot of sense. As tempting as it is to start running a bunch of trials, the results are going to be meaningless if you do not know what to expect. Additionally, research can be very expensive, so to get a grant a researcher will often need a clear, detailed, and interesting proposal. Fortunately, most of the materials I am probably going to be working with are relatively cheap, so it will not be the end of the world if I mess up. Still, I needed to do a lot of background research in order to create a proposal for my summer project.

I greatly improved my abilities on handling the drosophila from the first to second day. However, this was probably because I was moving faster and was a little overly aggressive. I accidently decapitated two of them; one incident was very rapid, while the other one progressed more slowly; without getting too graphic, it kind of got stuck fairly deep in the brush tool that we use to slide then and pick them up, and there getting its body out with its head intact was a pretty hopeless cause. Under the microscope, a beheaded drosophila can be a little intimidating. However, whenever I need any reassurance, I can always move back from the microscope and remind myself who’s boss.

I also learned another important lesson in the lab: always pay attention to what you are doing. Once I got distracted while preparing a sucrose agarose solution in the microwave, and heard a pop, which corresponded to the cap I loosely put on flying off, and solution spilling on the microwave (perhaps this might explain the sign on the microwave reminding no-one to try to warm up lunch there). Fortunately, my solution was mostly just sugar water. The important lesson I drew from this experience, though, is that *crap* happens, even in the lab. However, you can still try to learn from it. I should have heated the solution in a different flask than the bottle I used, but even more importantly, I should have been paying closer attention to my solution while it was heating. Diligent and careful work cannot prevent every mishap, but it can go a long way to preventing these kind of blunders.

Anyway, I hope you have found my post interesting.  The couple weeks of the lab are quite a learning expereince, so it is nice to be able to reflect upon everything. Anyway, hopefully by the next time I post, the Detroit Red Wings will be celebrating their second straight Stanley Cup!

I'll conclude with some pictures:

Summer reading doesn't end at high school.

My awesome mentor Lixian.  She is a fifth year grad student working toward her Ph.D.!

Me taking a break from pushing some flies.

My workspace...mostly after cleaning up!

"Time flies when you're having fun!"..even scientists have a sense of humor!

Crash course on identifying drosophila.

Incubators where I store my drosophila.

Genome Science Research Building I (aka Snyderman Building).  The bridge reminds me of the dorm Bell Tower, except the GSRB I Building is nicer!

(Hint to anyone who hasn't written yet:  Press "Save" like literally every 5 minutes when writing these)