Blogging about being a professional student, my love of science, being a Unitarian Universalist, becoming a foodie, living on the cheap, taking pretty photographs, books, and the importance of tea in my life.
The Great Apartment Hunt has begun. I live about 4 miles from my favorite part of campus, and around here, that pretty much equals the boonies. There's a sad excuse for a mall nearby, as well as a Friendly's and an Applebee's. OMG, how not exciting!
The plan is to move near downtown and campus. Then I'll be able to walk to school, friends' apartments, shops, and bars. I found a wonderful apartment that will hopefully be mine.
There are things I'll miss about the boonies though. I'll miss seeing every star in the sky on clear nights. As much as I complain about the deer overpopulation, I'll miss having adolescent deer standing in front of my window, searching for apples in the snow. I'll miss seeing a deer eat an apple.
And I'll miss having easy access to Target, purveyor of all things necessary for life.
This year for Christmas, I asked Geico for a new car door, and they said I could have one! I know that car doors aren't normal gift requests, but it's not often that car doors have gaping holes in them. Like mine does.
Zoom back in time to Friday. Friday was supposed to be a beautiful, glorious day. After talking about proteins and duckweed for five minutes, I would be done with Semester 1 of graduate school. There would be a celebratory lunch, then a drive to DC so that I could spend time with M in a wonderful city.
These plans did not include an epic snow storm occurring in Maryland and Virginia.
Side note: People warned me that driving in Pennsylvania could be dangerous. I might get stranded. I might end up living my life in Scranton, trying to sell bananas or something. All because Pennsylvania isn't known for their plowing prowess.
Pennsylvania had beautiful clear roads. Then I reached Maryland, land of non-cleared roads. And not salted roads.
I don't particularly like Maryland. Baltimore in specific. The last time that I drove through Baltimore, I went to McDonald's and told off an unattractive, aging, beer-bellied man for teaching teenagers about beer goggles. I already am biased, and the negative bias grows!
So there I am, on the outskirts of Baltimore, my not-favorite city that features not-salted roads. The snow begins to fall. I'm a Northerner now, so I declared that I don't fear snow.
What anyone should fear, though, is other people driving on snow. Especially ones with 4-wheel drive who develop megalomania and think their cars can handle anything. Not that I'm bitter or anything.
And so, I was driving on snow. My lane was fairly clear due to big trucks who had driven in it before me. The exit lane, however, had beautiful virginal snow on it. I got into the exit lane, and then I saw a Jeep facing me. Facing me on freaking I-695. That's not supposed to happen. The guy had lost control and spun out his car.
I hit my brakes and immediately realized that snow was going to prevent me from stopping in time. I then turned my wheel as hard as I could, heard the lovely scraping-plastic-on-metal sound, and came to a slow stop. My car is made of plastic, and much of the plastic on my passenger car door was missing.
My door was the bad news. The good news was that the other car was fine, my car ran, I wasn't injured, and my cat was not traumatized. (Did I mention the cat in the back seat?) It was still crazy dangerous outside, so we exchanged info and went on our merry ways.
Today I went to a coffee shop to study for my upcoming exam. The coffee shop is known for being run by a commune (or possibly a cult...), and interesting people gather there. I sat at the back of the shop, hoping that anyone who was there to chat and relax would sit near the fireplace and the windows. Sigh, no such luck.
I learned that one man is writing a book. We didn't converse at all, he just spoke to three other people about this book, and I really couldn't avoid eavesdropping. I wondered if he spent as much time writing as he spent talking about writing. Anyways, as I heard over and over, his book is about how he moved to a far away city to find himself, and while there, he came to the conclusion that our culture is too isolated, we should all live in communities or with our extended families, and that everyone should do experiments in order to find themselves. I found it hard to take him too seriously when I heard that he lives over five hours from his nuclear family, so he must still be pretty isolated, even after finding his true self and understanding the failings of our culture.
And here's where my science-y biases come in. I kept thinking that in the time it took him to move across the country and learn about himself, he could have been contributing to society by expanding the bounds of human knowledge. I already know about self-discovery because I've read Into the Wild and The Motorcycle Diaries. I felt his time could have been better spent preparing for a career in science or engineering, or in writing something truly novel. It didn't help that I was reading scientific papers that explained mechanisms of aging and cancer while listening to him.
And then I started thinking about how amazing science is. This man did personal experiment to learn truths about himself and our culture. The experiments I read about, though, described experiments that exposed deeper truths that don't just apply to humans but also apply to yeast, a single-celled organism. Want to feel connected to all of Creation? Then consider this. Everyone, from humans down to E. coli, use closely related proteins and pathways to make new DNA, repair that DNA when it's damaged, and turn that DNA into proteins that dictate our entire lives. I already know that culture is getting increasingly isolated and fragmented. Without that isolation, though, I wouldn't be at my current school preparing to further stretch our collective knowledge of life and how it works.
Sunday, December 6, 2009
What a stressful week. The tension in my shoulders was a constant, physical reminder of the week's emotions. Sadness at once again leaving my my loved ones in pursuit of an education. Frustration with being sick. Worry that nothing in lab will ever work for me again, leaving me with no meaningful data from the past two month. Sheer busyness from writing a 20 page paper with four other people. It was a long week.
And then the wonderful feeling of the tension melting away, like the snow melting outside, while singing and dancing to "Hey Yeah" with dozens of other people in an ill-lit bar.
It's a work hard, play hard existence here. I'm glad I found time to play yesterday.
Not too surprisingly, I lost NaNoWriMo. The goal was 50,000 words in the month of November, and I wrote 16,325. While I officially lost, I'm still happy with my effort. It's been a long time since I felt like I had a story inside me that I wanted to share with the world. The book is far from done, but it has been started.
Last February, I tried to write a novel about sailors and pirates. The main character, Amelia, grew up living the good life, but her father lost all their money, and the family ended up living in the slums of England. The father would do anything to try to make money, including pimping out his teenage daughter. Amelia ran away from home and joined a merchant ship while dressed as a boy. And then the story ended. I wanted it to be historically accurate, or at least more accurate than Pirates of the Caribbean, so I couldn't focus on the story at all. I was too busy asking, How many people live on a ship? How often do they sleep? What jobs could I give my novice sailor to do? How would Amelia hide the fact that she was a woman while on a very small ship?
I love pirates, and I hope to someday finish that story. Pirates provide a good vehicle (vessel?) for questioning identity and fighting against social norms. For now, though, I think I'll stick to my story that takes place in a coffee shop and explores the life of 20-something year olds.
My other writing plan is to write about my true love, SCIENCE. More precisely, I want to write about the people who did really cool science. In school, we learned lots of scientific facts but almost nothing about the art of discovery and the people making those discoveries. I think people are fascinating, plus I want to learn from those scientists who discovered amazing things. In that vein, I plan to look up information about Nobel Prize winners and share how they made their awesome discoveries. We'll see how that goes.
Some people have asked what exactly it is that I do during those hours I spend in lab. For that reason, I now give you an introduction to DNA methylation.
As you may know, DNA is made of up four bases: adenine (A), thymine (T), guanine (G), and cytosine (C). In the double helix, A always binds with T, and G always binds with C. After DNA is transcribed to form RNA, sets of these three bases are called a codon. Each codon codes for one of 20 amino acids. When the amino acids are linked together, you get a protein.
Not all DNA forms protein though. Within one gene, there are different regions, and only the exons actually code for proteins. A normal gene has an enhancer, a promoter, two untranslated regions, exons, and introns. The enhancer can be thousands of bases away from the actual gene, yet from that distance it can determine if the gene is regulates is turned on or off. The promoter is directly upstream where RNA transcription begins. In order to turn on a gene, the promoter must recruit RNA Polymerase II and other proteins used in
(image from http://en.wikipedia.org/wiki/DNA, created by Madeleine Price Ball)
transcription. The two untranslated regions are transcribed into RNA but they don't become protein. Instead, they help the mRNA move from the nucleus into the cytosol, and they are also involved in regulating the translation of the gene. Exons code for proteins, and they are interrupted by introns which are removed before the mRNA leaves the nucleus.
When a C is next to a G in the DNA sequence, the C can be methylated, meaning a -CH3 is attached to it. If the methylation mark is found in the enhancer or the promoter, it often means that the gene should not be turned on. It's stable, meaning that as the DNA replicates and the cell divides, the methylation mark remains in place.
My current lab studies these methylation marks, and so I do too. We detect them by treating our DNA with sodium bisulfite. Bisulfite has the power to turn C's into uracils (U, found in RNA), but it can't convert a C that is methylated. After the bisulfite treatment, it's possible to tell if any C was methylated because it will only still be C if it had a methyl group attached.
I'm working on extracting DNA from different types of cells and doing this bisulfite treatment. I'll eventually be able to use mass spectrometry to tell whether or not I have methylation in these different cells, and that's pretty exciting.
As an undergrad, I probably averaged 5.5 hours a sleep a night during the week and totally shot my sleep schedule to hell during paper writing season. When I hit Year 5 though, I'd had enough. I discovered that sleeping 7 hours a night felt amazing and as a bonus my coworkers stopped telling me I looked tired on a daily basis. Sleep apparently made me more attractive. Win!
Now I'm back in school, and the deal with grad school is that I could totally find work to fill every hour of every day. There are papers to read, notes to review, experiments to think about, exams to take. I could actually do all the required reading on time, deeply understand the papers I'm assigned for my discussion paper, become an expert in my field, and apply for every fellowship imaginable.
Just because it's possible to fill every moment with school doesn't mean it's advisable. I don't stress as easily when I sleep, which makes me happier. Grad school takes five years, and I'm determined to be a happy, less stressed, and get enough sleep.
At the moment, my only roommate is my cat Sapphire. He's a pretty good roommate, considering he can't feed himself or clean his bathroom. He's excellent at purring and making me feel loved when I get home from school.
Sometimes, though, I wish I had a roommate who was capable of cooking me dinner and running some needed errands. Last week was pretty overwhelming with my last-minute decision to apply for the NSF, and then I ran out of time to buy food or even cook food. I survived off of less than stellar campus food for lunch and fast food for dinner. It wasn't particularly healthy, tasty, or cheap.
This week, however, will be better. I'll even eat vegetables, which I hear are good for you. If I can find arborio rice in this town, there will be risotto just to make up for the McDonald's I ate last week.
It's only Day 5 of NaNoWriMo, and I'm already completely derailed. The derailing happened on Day 2, around 12:30 pm. At that moment, I decided I needed to apply for the NSF fellowship. I would be filled with self-loathing if I didn't at least turn in an application. That applications is, of course, due tomorrow.
I have been writing this week, which is half of the point of NaNoWriMo. I've just been writing about how I'm an amazing person and my plan for great research.
I will return to my novel tomorrow! I miss you already, novel of mine!
I got an email today from NaNoWriMo that was full of good advice for new writers. Things like it's okay to have no clue what I'm doing. Do not edit while writing. Write a shitty first draft and then edit it to my heart's content, but only after I have an entire first draft. And lastly, tell everyone I know that I'm writing a novel.
So here goes. I'm writing a novel. At the end of November, I should have written 50,000 words of a book. My personal goal is to write at least 2000 words a day. We'll see what happens!
I made a roasted chicken on Sunday. The entire 3 pound chicken cost under $6, and I'll be enjoying my chicken goodness for a few more meals. My future includes chicken pot pie and maybe even chicken & dumplings. Yum!
When I roast a chicken, I get very intimate with it. I like to melt butter, add spices to it (this time I used sage, marjoram, thyme, and rosemary), then coat my fingers with butter/spice mix, and rub it under the chicken's skin to add more flavor. I also brushed it on the skin and dumped the rest of the mix into the chicken cavity (after removing giblets because giblets=ew). Then I cooked at 350F for almost two hours. Delicious!
I saved the carcass in case I want to make stock. My last stock-making experience didn't work out though. Any stock-making advice?
I was informed by friends that talking about the carcass in my refrigerator made me sound like a serial killer. I swear, I only store chicken carcasses! Really!
I also made bread pudding, but I fear my bread:pudding ratio was off. Maybe next time will turn out better.
Today I went to class, took my first exam of the semester, collected the remaining shreds of my dignity, and went to my second class. Those shreds of dignity that I still had after the exam? They're gone now. I left them in Warren Hall this morning.
Some people are phobic about blood, graphic descriptions of medieval surgery, or large flying insects. Not me. I can handle all of those things just fine.
What gets me is eyes. Eyes are freaky. They're squishy and connect to the brain and talking about them is just gross. I could never wear contacts because, ew, I'd have to touch my eye to do so. I will wear the clunkiest Coke bottle glasses before wearing contacts.
So yeah, eye phobia. I have it. What did we talk about today? Retinablastoma, aka TUMORS IN THE EYE. The professor kept talking about these tumors and showed graphic, horrifying pictures, and I proceeded to flip the fuck out. I was shuddering, covering my eyes, and trying to fold myself into a fetal position at my tiny, tiny desk. And my classmate was laughing at me, course. I can't blame her because I was being totally ridiculous.
To add to my embarrassment, I sit in the front of the room. I'm in the Female Grad Student row. We're fairly well known now in the department. We all party with our TAs and talk to our professor outside class. My freak out was noted.
To date, I have spilled my tea everywhere, caused a potential lab hazard by attacking someone with hugs, and had an epic freak out, all in front of my departmental faculty. Excellent.
I recently read a book of short stories by Richard Russo called “The Whore’s Child." I’ve also read his books Empire Falls and Straight Man. All of his stories are about people who realize they’ve gotten trapped in lives they never wanted. Many of his protagonists decided to settle on something at one point, with every intent of fixing life later, but instead they stay in a non-fulfilling existence. His stories are scary because it’s easy to see how easy it is to lose control of your life. His novels are a bit cheerier because they’re longer, and his characters get a chance to change and create a new life.
Yesterday I read all of Julie Powell’s Julie and Julia and like Russo’s characters, Julie realizes she’s stuck in a life she doesn’t want. She hates her job and will probably never become an actress even though that why she lives in New York.. Plus she has a ticking maternal clock and a syndrome that makes it difficult for her to get pregnant.
So she turns to cooking. With support from her husband, brother, and friends, she cooks every recipe in Julia Child’s Mastering the Art of French Cooking, Volume One within the next year MtAoFC has 524 recipes. That’s a lot of cooking.
All that cooking was a true challenge. She probably used 200 pounds of butter while cooking organs, boning a duck, and vivisecting a lobster. There were many tears as aspics refused to gel and bone marrow did not easily leave the bone. Yet she seemed happier at the end. Even if she didn’t enjoy her secretary job, every night she what home and worked on a personal goal, one whose rewards included a full stomach and happy bystanders.
This book made me want to try new foods. For the first time in my life I felt a craving for liver and bone marrow. Seven considered asparagus. Maybe I’ll find myself a copy of MtAoFC and cook some new foods. I should be able find a reputable butcher in Ithaca My fellow students can either be entranced or repulsed my food adventurism.
Major parts of-the grad school application include recommendation letters, transcripts, and the personal statement. These are things you need to start working on early. I started my sophomore year.
For my transcript, I took classes in genetics, biochemistry, and cell biology. I got good grades in all my classes, so I had a 3.9 GPA when I filled out my applications. Good grades are very helpful.
Most schools require three recommendation letters. I had worked in two labs, so my two PIs wrote me letters, as did one of my genetics professors who had taught me a lot. Had I not spent much of my undergrad life in those labs, my application would have been much weaker.
For one thing, I had tried out different kinds of labs. I enjoyed the quantitative genetics lab that I had begun in, and I learned many essential skills there. It was in my second lab, though, that I found I truly loved molecular biology and gene expression.
For another, I had been in my second lab for over a year when P began my applications. My PI knew me very well, thought I did good work, and wanted me to get into an excellent program.
Working in one lab for a long time means you can do in-depth work on your project, impress your boss (hopefully!), and get a good idea for the research you want to do once you reach grad school. Between my project and all the literature reading I did, I knew I wanted to investigate gene regulation, transcription, epigenetics, and cell development
The personal statement asks what research you want to do. I had an answer.
As soon as you realize you might want to go to grad school, get research experience in your field. In the process, you’ll find out if you like research (which you hopefully will if you’re serious about grad school) and your application process will be so much easier.
Working in one lab for a long time means you can do in-depth work on your project, impress your boss (hopefully!), and get a good idea for the research you want to do once you reach grad school. Between my project and all the literature reading I did, I knew I wanted to investigate gene regulation, transcription, epigenetics, and cell development
The personal statement asks what research you want to do. I had an answer.
As soon as you realize you might want to go to grad school, get research experience in your field. In the process, you’ll find out if you like research (which you hopefully will if you’re serious about grad school) and your application process will be so much easier.
As you may know, DNA is made of up four bases: adenine (A), thymine (T), guanine (G), and cytosine (C). In the double helix, A always binds with T, and G always binds with C. After DNA is transcribed to form RNA, sets of these three bases are called a codon. Each codon codes for one of 20 amino acids. When the amino acids are linked together, you get a protein.
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