Why do this? Why write these? For fun - try new things - experiment - never done this before. Have to try things. I heard it's good to write a bit a day - this makes me write something - and then someday, maybe I can channel it into something more actually useful - instead of a blog ... a ... book? A paper? A something useful. Plus, I totally can't write very much right now, so these will be short. Maybe my verbosity will take over and betray that last sentence. We'll see.
Friday the 13th! A blessed day
Thursday: the day that vaporized and attack of cume doom
Mostly though, I want to sit in a dark corner and read papers. But I can't find any dark corners. Room 533 is taken over as office space. The library is of course also office space. I need to find a new study hole. Too many people walk around psychology for it to be a nice hole to hide in. In lab, if I really want to be serious, I find I'm easily distracted. Today, I listened to Vivaldi while studying - it's my favorite background white noise - but that gets mildly annoying after a while.
I went to the organic cume: I came, I saw, I flubbed it - I can put a check mark by "successfully failing cume." On Facebook, Daniel linked me Neo's first jump, which really made me smile - Daniel is the best. There were ten reactions we had to draw mechanisms for - I made a stubborn attempt on the first one for an hour, even though I had no idea, just to see if I could make anything plausible looking and I didn't want to turn in a test without a serious attempt on at least one question. All the reactions looked interesting - too bad I didn't know what they were. Wallace said he'd figured it'd be bad so he stayed the heck away. I told him what I tell everyone - come join the fail boat! - I feel certain that *looking* at cumes has some kind of mysterious magical or therapeutic effect.
Wednesday: imaging my gel; seminar; talking to people
It seems to me an incredibly lot happened today, hence the length of this note. I went to class, first of all - I almost forgot about that - man, that was interesting - I'm loving bioorganic. Dr. Weinert makes us really think and it's almost a class discussion about protein and enzymes, rather than a lecture. I'm enjoying the kinetics stuff more, because I can actually use it for my rtcB. Before, when I took biochem, I *hated* kinetics vitriolically. We're also talking about really fascinating stuff, like identifying the amino acids in an enzyme's catalytic site when you don't have the sequence! You can do all kinds of "old-school" chemical modification techniques to do this it turns out - I'd never head of the like. I'm impressed with the people who came up with all this and labored over experiments to figure this stuff out - I can imagine it really did take years and years. I told Dr. Weinert I was thinking of doing something with the NHEJ proteins and others that were involved in DNA editing for the proposal and she said that was fine with her.
After class, prepping stuff, panicking, then prepping more stuff
Between class and the seminar, I was furiously trying to pour a 15% gel and prep my samples, which seemed to happen really slowly. I had been worried in the morning that I might have annoyed Khalid by accident by trying to find another time for lab meeting, and when I saw he hadn't responded to my email I started panicking. Fortunately, it was all for nothing, as he wasn't mad, praise the Lord. I talked to him and everything was ok and he even seemed in a better mood than usual, so I slowly calmed down and went on furiously working - but I think panicking slowed me down, which was irritating. I also hadn't done this experiment in about two weeks, so I felt like I was not quite as efficient. But it all worked out. I just got a chance to eat lunch - turkey sandwiches, so good - before seminar.
Seminar, very interesting, professor from Harvard
Seminar was really cool. I was surprised more people weren't there. I texted a bunch of my classmates to come but a few of them either had lab TA or class going on - so maybe that's why. Khalid was talking to the speaker a long time beforehand and I wondered what about - professory things? It turned out yes - he said they were discussing the politics of universities. I'd say that counts as 'professory things.'
The speaker talked really fast and everything he said was interesting - I understood 80-85% of it - which is amazing, considering that's not often the case (it's always far easier for me to digest things I read than things I hear). He discussed how he was looking for tiny peptides in cells, back tracking them to the cellular pathways with which they interacted. He talked a lot about this insulin mechanism too, and NHEJ! Whoa - two of my favorite subjects right there - I was so pleased - some of the NHEJ proteins he mentioned I recognized from my weekend lit search, though I didn't know what they did until he talked about it - I'm going to make sure to read more about those. I copied down the interesting papers he mentioned.
After his talk, they asked if we had questions - and I felt as if I had a million half-formed questions squirming around in my mind like snakes, and a million half-formed thoughts and wrestlings to understand things he said - none of which could be sorted out fast enough. I was kind of wondering if those BAX/BAK proteins he discussed interacted with the mitochondrial membrane since the membrane deformed when they were deleted - but he only mentioned an interaction on initiation of apoptosis - weird - but I figure they must interact somehow, if their deletion results in deformation - so I thought maybe that question was too obvious. Khalid asked a kind of similarish question to that, I think. But it didn't end up answering my question.
After seminar, more experiment
I finished setting up the gel and ran it after the seminar. I saw Carol putting away paper towels from large boxes - I thought to myself - ah! so that's what those boxes had in them! I was wondering this. I asked if I could help and she said sure - so we both put them away - I'm glad we got more of those; they were really needed. Afterward, she said thanks a lot! And sounded happy! I felt as if I'd just gotten an incredible honor or treasure or something, being thanked by Carol! It's not easy to make her happy. The other people in lab are easier to understand. I didn't realize she appreciated help with things - so, I'll make sure in future, to just quietly come help her put away stuff or cart stuff. Now I know a new way I can be helpful to her. She likes efficiency.
Ian came in and I gave him the update. Unfortunately, I was an idiot and messed up his experiment by telling him the wrong protein concentration for that gel he ran - it was too low - I wanted to mimick the ligation conditions, but of course, I can't see that small amount of protein on the gel! *headdeskheaddeskheaddesk* I told him this and he wasn't much upset. He said he'd come in Friday to repeat it. At least he has that other gel he poured, so he doesn't have to pour another. And I explained how the RNA gels worked. I'm amazed the undergrads don't come in more frequently. When I was an undergrad, I came in every day, worked all day, studied at night, and only took off about two days before tests to study extra (during my last semester).
The classes must be harder at Emory perhaps. Ian says he's taking Pchem and advanced organic 2 - I'm really impressed with him for tackling those. I feel like he must be smarter than I am - I'm not sure what would happen if our roles were reversed.
Imaging the gel, talking to Yue, to post-doc
Yue came and talked to me a long time about RNA, and how did one prevent contamination? She said she was thinking about doing work on RNA and riboswitches for her post-doc. She also asked me lots of questions about SYBR gold dye that I use and I told her all I knew. She likes to talk, it seems. She also asked me about my project. She said a lot.
She went with me to image the gel because she wanted to see how the instrument worked. I had been praying the Lord would provide a way to get into Rollins because I don't have that key yet - I'm going to get one this week I hope - there's just been no time. Fortunately, the problem was solved, because Yue had a key to Whitehead - and it turns out - she knows secret passages to EVERYWHERE! It was amazing. When I went through Whitehead, the door to Rollins was locked - but she said - oh, it's only locked on the first floor - on all the other floors, the connecting tunnels are open! And she told me about a secret door to get into Atwood too. She talked almost non-stop all the way there and back - she didn't monologue - it was a real conversation pretty much, though I didn't talk as much as I could have, since I was tired, but she'd keep talking anyway - I can't believe anyone would want to talk that much.
Before we left, the post-doc who'd been working in our lab asked me questions about RNA - I felt honored he'd ask me anything - he'd heard Yue and I talking. He probably wouldn't have talked to me maybe if he knew I was just a 1st year. He said he was doing a project isolating HIV RNA - but I wasn't that helpful because I didn't know about the techniques he was doing. But, I did tell him about my former grad student friend Mark Stead who now works in NY, Einstein College. He patented a new technique to isolate RNA - REALLY fast and efficiently - and gets amazing yield too. It used to take 2 days. His method takes 20 minutes or less. Mark is amazing. The post-doc copied down his name to look at his paper later. He talked so quietly I could barely hear him and missed half the things he said - I really wish he would have spoken louder. I kept inching closer to him to hear better but it didn't help much.
We imaged the gel. I sent info to Khalid. The gel was partially successful but the 10mers are missing again. I got an email from the Tech guy who sent me lots of great papers. I looked up papers by Dr. Gao - oh man does he ever have some cool ones! I can't wait to read more of those - more stuff on Cas9 even, DNA editing, using NPs for drug delivery - jackpot right there, OH yeah. So, Yue and I talked all the way back to Atwood and now I know a lot more about her. I always thought she was kind of odd, but I liked her better after today. She talks to me like an equal even though she's a 5th year. We talked a lot about different jobs we thought were ideal after grad school and why, and various thoughts about teaching.
FIN, more disorganized and random, as I get more tired
On the way home, I blared my Celtic/Irish music - The High Kings - for the win! Especially after a busy day, that's my favorite music to listen to a lot of the time - it's really relaxing. I've always thought almost strange that I enjoy it so much considering that one quarter to one half of the songs on their albums are drinking songs, and John and I don't drink. Is this even appropriate? I don't know. It's just fun music. I've thought a lot of thoughts on that, none of which are worth writing about. Sometimes, I wonder if everyone thinks so many thoughts all complexed together and simultaneously, or if that's just me. John likes bag pipes a lot - they are practically his favorite instrument. I like them less so - too screechy - but sometimes they can sound ok.
I got home late and mom and dad left me out a plate of fish, corn on the cob and rice neatly wrapped. I devoured the corn in under 30 sec. I love corn on the cob. I ate half the fish. I'm so thankful to my parents for helping me with food - I can't decribe how thankful. They make my life a lot easier. I'm way spoiled.
I was so happy to see John. He'd had a rough day. Now, I'm going to sleep. I've stayed up way too too late writing this silly long note, but there was a lot that happened today, and for some reason, I just felt like writing about it and didn't want to leave anything out because it was all interesting. But, I really need more sleep. I'm going to sleep in tomorrow. I've discovered it takes me about 1 hr 20-30 min in the morning to get to Emory and about 45 min exactly to get home, when there's no traffic late at night. Longer than I thought it was. I'm planning on taking the organic cume tomorrow and fail it so I can get used to failing those and just see what one looks like, because I'm curious. And that, is all.
Tuesday: microscope seminar, Wallace/Keon, lab meeting
Very tired, though today was a pretty good day - felt really long - which was weird, because yesterday felt so short. Went to a multiphoton confocal microscopy seminar in the school of medicine just because - was hoping it would introduce me to more technical aspects of microscopes, even though I suspected our lab didn't use that kind. It was an interesting talk and the instrument made very pretty pictures. Afterward, I talked to one of the people who stayed behind - and it turned out to be Alexa - I was like, OH! Hi! She's Daniel's collaborator on his microscopy project. I've heard a lot about her. She said I could come by tomorrow to see the scope work if I wanted.
Later, Daniel updated me about his project in more detail. I understood it a bit better and he was also able to answer some dumb microscope questions for me that made that seminar I went to make so much more sense. I think I now understand better the differences between TIRF and confocal, their advantages and disadvantages.
In between, I was able to setup a ligation reaction for the hybrid substrates. There was another seminar somewhere else, but I didn't want to go to two in one day, so I skipped that one. Keon came and talked to me a while and I showed him the lab; then Wallace came, and talked a while about his NSF idea, while I was calculating concentrations of my DNA.
Lab meeting was interesting - I liked Carol's papers - they were unique and unusual. Yoshie's data was interesting but I was having trouble understanding it for some reason. I have a few questions - I'll have to ask her later. There was pizza - I'm so glad - because I was hungry.
I'm hoping we can get lab meeting moved earlier. Right now it's at 7 p.m. There was some intense negativity from 1/2 the lab when this switch was made, which really annoyed me - Khalid rightly said that it's just b/c of schedule conflicts. He's not trying to frustrate ppl. All we need to do is see if ppl's schedules can accommodate an earlier time. Khalid was ok with me collecting them, just finished that today, and I think we have some open slots! Here's to hoping. Maybe there's some other reason an evening time is important that I didn't account for. If it doesn't work out, that's ok - we do what we have to. I've warned John about all these late nights and he said the above statement. It'll all work out in the wash. Likely any time is bound to frustrate somebody - you can't make everyone happy. To this one though, it seems such an easy fix.
I thought about trying to switch my Monday lab TA that's at 6 p.m. to Friday at 6 p.m. - Khalid said that time was really despised and I figured it might be the only one I could swap for, but alas, there's no labs on Fridays for orgo. John does a gaming thing Friday nights, so at least he wouldn't be alone, if I had labs then. But I've warned him about this and he says it's ok - we have to do what we have to do. Right now, he's just been typing out the story of his new RP character, Gortlomozomog, the slightly insane goblin who thinks he can talk to animals - this is goblin, as in World of Warcraft variety, not Lord of the Rings.
I'm excited to see what the gel looks like tomorrow! Also, I ordered DNAzymes and a substrate today for cool in vitro experiments happening soon. Ok, to bed I go.
Monday: First TA slot; working with Ian
I can feel it happening again - total absorption by SCIENCE. I have absolutely no room in my head to think of anything else - and that's ok with me. I like science. Coming home is jarring because it reminds me something else exists. If I think anything else, it's very small, and usually in the morning when I pray about stuff and - ask the Lord to help me learn more SCIENCE.
Quasi-grad student mentor
Today was incredibly busy and felt really weird, but was interesting. Ian came to do experiments and I showed him the protein gels. I felt almost as if I were a grad student mentor, which I guess I am, which is weird. I've never been one before. I was thinking of all the things that I didn't like as an undergrad being mentored and hope I can do better, but today, I just felt so terribly unorganized. I shall keep trying. I have a philosophy on this I've been trying to build. We'll see if it works or not. I thought a lot of complex thoughts about this simultaneously, which I could try to convey, but it would take 10 pages, so I won't. That's very annoying, on the whole, by the way. Because I want to write all of it. But, what purpose would that serve? No one would read it. It'd be boring as crap. Maybe to organize my thoughts. [ends philosophical rabbit trail]
First Day of Lab TAing
Got to go to the lab TA thing, which was at first scary, because I had no idea what to expect, but ended up being interesting. Christian was there, which was comforting. I really enjoyed Mr. McCormick's lecture. He did an amazing job communicating the lab in an interesting and relevant way. It felt bizarre to be on the other side of things. I've been so before many times at Oxford, but here the class is so much bigger, and the bigger the class, the more distance there feels like there is from the students.
While sitting there listening, I had a bazillion thoughts pouring into my head, about teaching labs and organic chemistry, some of which were wondering if it were possible to teach well this many students organic chemistry simultaneously (I'm skeptical), and if so how? and why didn't Mr. McCormick mention more details about the theory? (he did later, and I was relieved) and I wonder if it could be done better, if these other 4-5 things were done? and I wonder how I can ask questions to students in a less abrupt way that doesn't scare them - otherwise, I might be like Dr. Lynn - Dr. Lynn seems to me to ask questions that somehow drive all logical thought from my mind and I have no idea what the answer is. That's the kind of look these three students gave me. And I thought - oh no! I can't ask questions like that! I'm becoming like those scary people! Hmm. *wheels turning* Altogether too much thought was happening, and I had fun - it was interesting. And about ten students stayed to ask questions to Mr. McCormick which made me really happy that students are around who actually want to know the material.
Fin, amazing enzyme article
And then I came home and read the most interesting article Dr. Weinert gave us!! Enzymes are super cool and so completely amazing - there are no words to describe how amazing they are! I'm trying to figure out how to read more. Mostly, I just need to figure out how to organize and survive everything. Lots more happened, but that's all I can say for now. I hope there's food at lab meeting tomorrow. Hmm. I have to buy more turkey. Yeah, this is too long - and disorganized - this method might be another bust. We'll see.