Grad school is supposed to get less overwhelming eventually, right?
Ok, good. Just checking. Classes are actually not bad! It's just everything else that's the problem: reading papers to be caught up in my field. Finding papers to be caught up in my field. Meeting with my advisor. Emailing XYZ person about their research/training/meetings. Keeping my assignments straight. Finding time to do dishes/laundry/house-cleaning.
This weekend has been a long spate of procrastination (which is why I'm blogging and not working on a fellowship application), but good! I had my lab mates over for dinner and studying last night, which was a lot of fun. And now that my stipend is figured out (long story short, the Grad College dropped the ball and my monthly income came in a week and a half late), I can go stock up on sweaters because it's cold here already! Nothing too exciting going on here otherwise.
So, I've said a lot about the kinds of research projects my lab does, but you're probably wondering what I am actually doing in lab. I mean, all I'm doing right now is working on the California tribe samples, but surely there's a bigger project for me in might, right? Surprisingly, we should already have a thesis project idea. I was not expecting that. Luckily, I found something that I'm really interested in!
My project (as of now - things can change!) is studying dog domestication in North America.
Dogs? Not what you were expecting, right? Doesn't the lab do humans? Didn't I want to do research on humans?
Well, yes. But DNA analysis is DNA analysis. My professor has worked with macaques before, and one girl in lab is researching capuchins. And my research is related. There's a huge Native American ancient city called Cahokia near St. Louis that is being excavated. And in one of the nearby sites, they found 40+ dog skeletons! All of them predate European arrival in North America, so they are 100% Native American dogs. And some of them have viable DNA, which is awesome.
The current plan is to study these dogs to see where they came from. Did they come over from Asia with humans? Or did Native Americans domesticate North American wolves once they arrived? The last study done suggests that the dogs migrated over from Asia, too, but that was ten years ago and nobody has really looked into it much since then. It will be interesting to see what results I come up with!
Dogs are an interesting problem, I think, because they're so weird. Genetically, I mean. Any dog breed you can think of is only about 200 years old. So all of their history before the Victorian-era breeding craze is a little muddy. Working with old samples gives you a (slightly) clearer view of how things were before humans did too much meddling with dogs. There are a lot of other really interesting things about dogs that I've learned all the way, but I'll leave those for later. :)
Have a good week!
Sunday, September 23, 2012
Saturday, September 15, 2012
Problem Solving
One of the first things you learn as a researcher in a life science lab is just how unpredictable your results can be. Unlike physics research, in which things follow all sorts of defined rules (with the exception of quantum mechanics, but I'm sure they have their own rules), or history, in which you're browsing old (and constant) sources, life science labs depend a lot on living things, and they don't like to follow instructions.
Of course, our lab is better off than a lot of other labs, in that we generally just deal with DNA. We don't have to worry about picky bacteria or wilting plants or mice that don't respond the way you expect them to. But we still use "living" enzymes to do some of our work for us, and DNA can do weird things sometimes, too.
Sometimes, when our experiments mess up, we can blame ourselves. Maybe we didn't put in the right amount of something, or forgot to mix the samples well beforehand, or overmixed them into suds of broken, useless DNA (not that I have done that or anything...). And contamination is always a possibility - we are made of DNA, after all! However, no matter how perfectly you can follow instructions, sometimes things just don't work. And when that happens, you get to troubleshoot. That's often a large component of lab work, and pretty much the story of my week.
This week, we were working on getting a lot of our samples sequenced. Sequencing is expensive, and the more samples you can do at once, the better. On the way to sequencing, there are several steps involved:
Once we figured out that the PCR process apparently didn't work, we redid it on Friday and ran another gel. Thankfully, we had good results on Friday afternoon. We still don't know why it didn't work the first time. But after 3 hours in lab today, all of our samples are prepped and ready to go for sequencing! So I'd call it a success.
Over all, this process can be completed in probably 2 days of lab work. Instead, we were working on it for a week and a half. And while things are not working, all you can do is think of what could have gone wrong - did I make a mistake? Should I redo the extraction/PCR/purification? Are there any old chemicals I'm using? It can really be a pain to try and figure out what went wrong.
And then sometimes, without you doing anything differently, it all works. And you get lucky! I'm certainly glad we did on Friday - better late than never!
Of course, our lab is better off than a lot of other labs, in that we generally just deal with DNA. We don't have to worry about picky bacteria or wilting plants or mice that don't respond the way you expect them to. But we still use "living" enzymes to do some of our work for us, and DNA can do weird things sometimes, too.
Sometimes, when our experiments mess up, we can blame ourselves. Maybe we didn't put in the right amount of something, or forgot to mix the samples well beforehand, or overmixed them into suds of broken, useless DNA (not that I have done that or anything...). And contamination is always a possibility - we are made of DNA, after all! However, no matter how perfectly you can follow instructions, sometimes things just don't work. And when that happens, you get to troubleshoot. That's often a large component of lab work, and pretty much the story of my week.
This week, we were working on getting a lot of our samples sequenced. Sequencing is expensive, and the more samples you can do at once, the better. On the way to sequencing, there are several steps involved:
- Extraction - pulling the DNA out of your cell samples - in our case, cheek swabs or saliva samples. You can then measure the concentration of the DNA you collected.
- Amplification - making more copies of the DNA you want using PCR, a method using enzymes that copy DNA and heat cycles. You can verify that it worked by running a gel of your samples.
- Purification - getting rid of the DNA you don't want. Again, this uses an enzyme and heat
Once we figured out that the PCR process apparently didn't work, we redid it on Friday and ran another gel. Thankfully, we had good results on Friday afternoon. We still don't know why it didn't work the first time. But after 3 hours in lab today, all of our samples are prepped and ready to go for sequencing! So I'd call it a success.
Over all, this process can be completed in probably 2 days of lab work. Instead, we were working on it for a week and a half. And while things are not working, all you can do is think of what could have gone wrong - did I make a mistake? Should I redo the extraction/PCR/purification? Are there any old chemicals I'm using? It can really be a pain to try and figure out what went wrong.
And then sometimes, without you doing anything differently, it all works. And you get lucky! I'm certainly glad we did on Friday - better late than never!
Thursday, September 6, 2012
First Two Weeks!
Hello! I was honestly planning to post a big review of my first week of grad school, but the adjustment to busy days hit me a little harder than I had thought it would! I was going to bed by 9:30 or 10 most nights. However, a new post is long overdue. So here we go!
My first two weeks have been really full, but really good. I've started training in my lab, going to classes and doing all the social things that being part of a graduate department entails. Between my classes, lab meetings, reading groups and just generally getting acclimated to Illinois, I feel like I'm running around all day!
I am so excited about the lab I am in. I love all the people, for starters. My advisor's lab has one post-doc, four graduate students, and one undergraduate assistant who is just starting out. Of the graduate students, three of us are first-years! It makes my classes and lab time a lot of fun. We are from completely different research backgrounds - one girl worked in this lab as an undergraduate, and the other spent several years working in a similar lab in Pennsylvania before going to graduate school. In a way, I feel very under-prepared for this kind of work when I'm compared to the two of them! However, they're really nice and we all get along really well. And my advisor is really great as well - he's very hands-off in terms of letting his students be independent, but he is always available to answer questions when we have them.
The research they're doing is really interesting, too. The lab mainly works with Native American tribes - the project I'm helping with now concerns a tribe in California. Rather than just "using" their information for our own goals, the lab really works with the tribes to try and find out things they are curious about, too. And every summer, my lab does an outreach program where we teach teenagers from this tribe how to do the sort of work we're doing. Often, we're trying to figure out how much European admixture is in the tribe - did they interact with Europeans at all? There are specific sequences we can look at to determine the region of origin - Europe, Asia, or Africa. In a few weeks we will be able to send off several samples - including mine - for sequencing to learn more about where our ancestors came from thousands of years ago. Being able to work with my own DNA is really cool.
Class-wise, I have just a few courses but a whole lot of seminars. Class-wise, I'm taking statistics and population genetics. Both are review courses, but I think they will be much-needed. Plus, as part of statistics I have to learn SAS, a programming language. Considering my (mostly-failed) attempt to learn Java in high school, we'll see how that goes! Seminar-wise, I have the weekly talks the whole department goes to, a semester-long orientation seminar that tells us how to be grad students, and a reading group that covers all sorts of topics I've never looked at before.
All in all, I'm really enjoying grad school so far! The hours are long and expectations are high, but I know I'm at a great university and - even better - the best place for me.
My first two weeks have been really full, but really good. I've started training in my lab, going to classes and doing all the social things that being part of a graduate department entails. Between my classes, lab meetings, reading groups and just generally getting acclimated to Illinois, I feel like I'm running around all day!
I am so excited about the lab I am in. I love all the people, for starters. My advisor's lab has one post-doc, four graduate students, and one undergraduate assistant who is just starting out. Of the graduate students, three of us are first-years! It makes my classes and lab time a lot of fun. We are from completely different research backgrounds - one girl worked in this lab as an undergraduate, and the other spent several years working in a similar lab in Pennsylvania before going to graduate school. In a way, I feel very under-prepared for this kind of work when I'm compared to the two of them! However, they're really nice and we all get along really well. And my advisor is really great as well - he's very hands-off in terms of letting his students be independent, but he is always available to answer questions when we have them.
The research they're doing is really interesting, too. The lab mainly works with Native American tribes - the project I'm helping with now concerns a tribe in California. Rather than just "using" their information for our own goals, the lab really works with the tribes to try and find out things they are curious about, too. And every summer, my lab does an outreach program where we teach teenagers from this tribe how to do the sort of work we're doing. Often, we're trying to figure out how much European admixture is in the tribe - did they interact with Europeans at all? There are specific sequences we can look at to determine the region of origin - Europe, Asia, or Africa. In a few weeks we will be able to send off several samples - including mine - for sequencing to learn more about where our ancestors came from thousands of years ago. Being able to work with my own DNA is really cool.
Class-wise, I have just a few courses but a whole lot of seminars. Class-wise, I'm taking statistics and population genetics. Both are review courses, but I think they will be much-needed. Plus, as part of statistics I have to learn SAS, a programming language. Considering my (mostly-failed) attempt to learn Java in high school, we'll see how that goes! Seminar-wise, I have the weekly talks the whole department goes to, a semester-long orientation seminar that tells us how to be grad students, and a reading group that covers all sorts of topics I've never looked at before.
All in all, I'm really enjoying grad school so far! The hours are long and expectations are high, but I know I'm at a great university and - even better - the best place for me.
Wednesday, August 22, 2012
Hello!
First post time! :) I figured this would be an easy way to keep people up-to-date on my life in grad school (especially since so many of you are so far away!).
Let's start with the acronyms. I am starting my first year of graduate school at the University of Illinois, as part of the PEEC graduate department. PEEC stands for "Program in Ecology, Evolutionary Biology, and Conservation Biology", and is essentially a conglomeration of a lot of different professors with a lot of different biological interests. I'm here to get my Ph.D., and I'll be here for the next 5-6 years. I am also an IGERT (Integrative Graduate Education and Research Traineeship) scholar, which is an interdisciplinary program sponsored by the NSF. More on that in a minute!
I am going to be working with a professor who does genetic anthropology work - using DNA to learn more about our history as humans. The goal of genetic anthropology, essentially, is to figure out where a group came from, how they got here (geographically speaking), and what other groups they encountered on the way. It's a field I'm really interested in, so I'm excited to be working in his lab!
Due to my IGERT status, I also have another focus. The program is called Vertically Integrated Training in Genomics, and it's essentially teaching us how to look at an organism from the ground up: from their DNA to anatomy and even to higher-level functions like behavior and social organization. Working with DNA, you don't always get the chance to see the "big picture" of an organism, so that will be a new and cool experience for me. The best part, though, is I get to spend my spring semester in Panama, working with scientists at the Smithsonian Tropical Research Institute! I don't know much about it beyond that, but I'm looking forward to living somewhere new for a while and getting some more research experience!
I moved up to Champaign almost 3 weeks ago (we're not going to talk about the moving experience!), and I really like the town so far! In some ways, it feels a lot like College Station, because it's so small and everyone is so friendly. I already found a phenomenal Thai place and a Sunday night Pub Quiz and have been to the library more than once (and it's fantastic!), so I'd say I'm adjusting nicely. And the weather is amazing right now - it's 84 degrees right now, which is the high for the day. There are definitely things I miss about Dallas and College Station, though.
There's not too much going on yet; I start training in lab tomorrow and classes start Monday. I think I'm ready to get going! It's just another school year...right?
Let's start with the acronyms. I am starting my first year of graduate school at the University of Illinois, as part of the PEEC graduate department. PEEC stands for "Program in Ecology, Evolutionary Biology, and Conservation Biology", and is essentially a conglomeration of a lot of different professors with a lot of different biological interests. I'm here to get my Ph.D., and I'll be here for the next 5-6 years. I am also an IGERT (Integrative Graduate Education and Research Traineeship) scholar, which is an interdisciplinary program sponsored by the NSF. More on that in a minute!
I am going to be working with a professor who does genetic anthropology work - using DNA to learn more about our history as humans. The goal of genetic anthropology, essentially, is to figure out where a group came from, how they got here (geographically speaking), and what other groups they encountered on the way. It's a field I'm really interested in, so I'm excited to be working in his lab!
Due to my IGERT status, I also have another focus. The program is called Vertically Integrated Training in Genomics, and it's essentially teaching us how to look at an organism from the ground up: from their DNA to anatomy and even to higher-level functions like behavior and social organization. Working with DNA, you don't always get the chance to see the "big picture" of an organism, so that will be a new and cool experience for me. The best part, though, is I get to spend my spring semester in Panama, working with scientists at the Smithsonian Tropical Research Institute! I don't know much about it beyond that, but I'm looking forward to living somewhere new for a while and getting some more research experience!
I moved up to Champaign almost 3 weeks ago (we're not going to talk about the moving experience!), and I really like the town so far! In some ways, it feels a lot like College Station, because it's so small and everyone is so friendly. I already found a phenomenal Thai place and a Sunday night Pub Quiz and have been to the library more than once (and it's fantastic!), so I'd say I'm adjusting nicely. And the weather is amazing right now - it's 84 degrees right now, which is the high for the day. There are definitely things I miss about Dallas and College Station, though.
There's not too much going on yet; I start training in lab tomorrow and classes start Monday. I think I'm ready to get going! It's just another school year...right?
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