Monday: TAing orgo lab and making glass capillary tubes
Tuesday: lab meeting and stuff
Conticello's class was interesting. I found out from Morgan his proposal abstract is due NEXT WEEK. O.o Glad I found that out now. I didn't put his syllabus on my calendar yet. We talked about RNA structure - it was fascinating - lots of fascinating points were mentioned. And, something interesting happened - the Lord taught me the structures, somehow.
I've had trouble memorizing DNA/RNA structure. I've memorized them about three times and forgot them again. But Dr. Conticello had their structures on one slide. It was only up for a minute and I was staring at them. I don't remember what he said, but suddenly, patterns jumped out at me, as if in neon lights: I saw how the structures were oriented for their H-bonding interactions. I saw how the bases were always bound to certain N's and how they kind of moved around their axis. And the groups on the bases match and are reciprocal - it suddenly made sense - light bulb moment. The slide was gone. And I drew out the structures from memory on the spot, though I did get one residue on uridine wrong. I was like ... wow ... thanks Lord. I never noticed most of that stuff before and certainly not in that way. Let's see if I can remember it tomorrow. I think I CAN!
Oh, and Dr. Conticello showed us the most AMAZING animation of DNA replication from HHMI. I swear - I LOVE those SO much. Those kinds of videos are what inspire me to want to learn programs like Pymol (though that video was much more complicated than Pymol could do). Dr. Conticello also looked much happier today - he was smiling, looked stronger - it made me feel better - perhaps our prayers helped. I told my mom and she was praying for him too.
Lab meeting was really, really cool, because Kevin was presenting - and that was fascinating. He presented two articles on nanowalkers and one on enzyme enhancement for scaffolding - important for my project. I'd read the paper and I really need to look it over again and discuss it with him.
Zheng presented his data - it was fascinating - but unfortunately, my mind was getting fuzzier and fuzzier, because I was so very tired. I don't know why I get so tired at 8:30 p.m. It felt more like 10 or 11 p.m. to me. I think also, some of the things and detailis of what Zheng is doing is still hard for me to understand. I'd try to explain his data, but I don't have time right now.
I always look at the floor when I'm thinking and it seemed to me Khalid had on different shoes. I don't know if it's my imagination or not, but he appears to have a lot of shoes. I've noticed what I think must be several different kinds. And they usually seem to match his clothes. I must be imagining it. If it's true, that'd be pretty funny and more coordinated than I'd expect of him. That never happens to me except by accident. And I never change my shoes - though mom *made* me get a second pair of sneakers - so that I can trade them out and they have a chance to air out. Both are the *exact* same kind and look *exactly* alike. Once I find shoes I like, I get particular.
The topic of undergrads came up after lab meeting - and I thought about it some more. Ian is very truly the most consistent person we have working as an undergrad in the Salaita lab so far - but since he's working with me, I want him to be the best of the best he could be. He comes in W and F and has done so for the past about three weeks - only a couple times he came a lot later than he said and one time he left because no one was there (we were all at Korin's seminar). His classes are *really* hard too. I respect Ian a lot for his competence and making the effort to be in lab - he's been talking to me seriously about setting up our schedules better and he's going to make an even bigger effort to come in when he says - which is usually at 1 p.m. It's Rohan and Arish that frustrate me. I'm very glad Rohan was able to make it to lab meeting today - impressive, considering the hour. That would make the 3rd time I've seen him in lab or otherwise this semester so far. Daniel didn't see him at all but I told him - yes - he's been in lab twice. Perhaps I missed some other times. I haven't seen Arish at all - but I am not sure I know what he looks like. Maybe he's come and I didn' t know - that's possible.
I measured the time it took me to get home since Khalid asked and I didn' t know. It was exactly 42 minutes. And it appears to be about 25.4 miles between here and Lawrenceville. I didn't know that either.
He mentioned a cool podcast I should look at ... crap... what was it called, what was it called? It'll come to me. What I do on commutes is very dependent on my mood. Lately, it's been praying or listening to music. I used to listen to audiobooks, but I found it diffuses and unfocuses my mind too much - I only do that if I feel I need to escape reality for a while - which hasn't been necessary up to this point (at UGA, it definitely was necessary sometimes). I've also listened to podcasts - Science Friday, a few others - I haven't found any I love yet and it takes an annoying amount of time to look for more. It's just not high enough on my priority list right now.
And that's about all the science for now! There's some in God blog, here.
Wednesday: chemical biology seminar
I've addicted Daniel to the cookie clicker!! And three of my friends in WV. And there's nothing in God blog because I deleted it. I wasn't sure He wanted it there yet. I'll probably wait til weekend to post those or at least until I can know for sure. I only want to do what He wants.
I got to Dr. Weinert's class late, very unfortunately - I hate that - I have to make sure and leave appropriately early. There was a special case of gridlock due to three separate police cars either arresting people or servicing fender benders. It happens. I left too late.
Happened to hear Khalid and this visitor I saw in the morning speaking Arabic. That was fascinating. Khalid's English is so amazing, it's easy for me to forget it's not his first language. I never listen to Arabic. I would have liked to listen out of sheer intense curiosity but I couldn't for longer than a minute, because I felt like I was eavesdropping, even though I had no idea what they were saying.
Prayed for things, as God lead me to. Went to work on HW with Morgan and Gokul - we made some breakthroughs on problems #4. Just one more to go. I had to leave for 30 min and set Ian up on the gel situation, then went back to doing that.
Went to seminar - a professor from UC Berkley in Chemical Biology. I'm amazed by all the prestigious people we get to hear speak. I feel as if I should make more of the opportunity but am at a loss how to do so at this time.
She talked about modifying cellular pathways to produce materials like fluoronated drugs. It seemed a perfect lecture to listen to, in relation to Bioorganic, because it dwelt with understanding enzyme mechanisms in some cases and how they went about testing these things. She also talked about modifying organisms to biosynthesize n-butanol. She talked really fast. When thinking about how much work they do, I can understand why they would - who'd want to leave stuff out?
Chemical biology likes to deal in pathways, it seems. This is not my favorite subject. I haven't found a reason to like it yet. Like redox chemistry or enzyme kinetics, I feel as if I'd need a reason to study it or find it interesting. But I did appreciate listening to this talk.
Ian poured a beautiful gel. No bubbles or anything! We ran it and we got bands in all the lanes but I'm pretty sure they weren't separating. Frustrating, but at least the bands appear to be there.
Ian and I got to talk on the way to Rollins and I got to hear about why he wanted to be a dentist. It all came down to stability - he said, as a doctor, one could get into stress of life and death scenarios or late calls; but a dentist had good hours, decent pay and didn't have to think about work all the time. I asked him why science and he said he liked it, and he didn't want to do business, because his dad was a businessman and all his work friends were always so driven and crushed with work, working stupidly late hours, slaving away for money and they were very grumpy, unhappy people. He didn't want to be like that. Understandable. He said he'd rather be stable and happy.
I cannot understand choosing a career for the sake of stability. On the one hand, it's very logical and makes sense. On the other hand, it doesn't make any sense. Does this mean I don't like stability? No, that's not it. I couldn't untangle this philosophical riddle, of why this made no sense to me and why I could never do that. I do what I do because I love it and that's it. No other reason. Money, stability or whatever else matters not. It sounds to me like Ian thinks stability = happiness. Unfortunately, this is not the case. Not even research = happiness, as a foundation for it, I mean.
I left at 6:30 and got home. I told mom about Dr. Salaita speaking Arabic and she said,
"You should learn Arabic!"
"Because you're working for him. And then, you'd always know what he's saying."
"But mom, that's like saying, I should learn Chinese because half the lab speaks it."
"Yes you should!"
(...) *facepalm* You'd have to know my mom. She enjoys making these slightly illogical conjectures. Sometimes, I can't tell if she's serious or not - I think she actually is - she's just not thinking, at the time, of the practicality of what she's saying. It's ok - I don't mind - we have funny conversations.
She said, what, you like languages. Maybe. But I've never made a *serious* attempt at one. Except maybe Spanish - that was semi-serious. The the problem is, if I really wanted to learned a language - it would have to be all or nothing - which means I'd have to learn *one* fluently. That's a tremendous lot of energy expenditure for little gain. I wouldn't have the will for it and I could spend my time better. I'd only learn a language if I thought I'd use it consistently on a regular basis and I actually needed it. Spanish is the language I studied in college; therefore, I feel compelled to stick with it. It's the most likely to be useful, I figure.
And I'd have an equal interest in learning ... Spanish, German, Hebrew and Ancient Greek. Add Latin and Arabic if you want. I don't think that's happening. Nope. My interest in languages is far too diffuse and unfocused to be useful.
I had to return to Emory because I forgot to leave my key to the Typhoon instrument for Yue - completely my fault. She was about to run an experiment. I was really quite depressed about this for a while - the loss of all my treasured study time. But maybe it'll help me remember and not forget again. I feel like if I say something, I should make sure to do it. I got to pray with Esther on the way. Maybe the Lord knew I needed more prayer - it was good for me. And I had wanted to sing to more of my music. So on the whole, it got turned to a good end.
Now I'm very tired, in more ways than one. But I have to say, God's been really good to me. I could be really stressed. But I'm just not. I've reached that point past which additional stress doesn't matter. However, it would not be possible to be so completely unstressed unless God were doing it. I'm a pretty stressful person on the whole. I think He's doing good things and I know He's taking care of me. There's not much more I can say at present.
I probably won't be in lab much tomorrow. I'll just be working furiously on my assignments elsewhere. I detect a pattern here I might have to fix. I actually wasn't planning on doing experiments at the beginning of this week but then I said ... I'll just do one little one. I'll just do one more. I just have to help Ian image. Oh. Wait. Deadlines?? Where'd all my time go?? Oops. It wasn't supposed to take that long.
There's a lot of songs I want to add up here eventually but I don't think I have time tonight.
Thursday: quiet day, in which the Lord encouraged me
What I chose for my proposal
I had looked at proposing something about the rtcB mechanism, and while there is some argument about it, it’s really well studied. I decided against it, because I realized, I only enjoyed describing detailed enzyme mechanisms, not proposing research about them.
I looked studying NHEJ, but there were so many unknown processes to choose from, and once again, it wasn’t necessarily my passion.
Last week, it suddenly became obvious what I should propose about – protein coronas around nanoparticles, of course! THAT fascinates me. I ran it by Dr. Weinert and she said I could do something related to that, but it would require a lot more reading than the rtcB idea. Yeah. Somehow it always seems to fall out that I pick the route that requires more work. But I figure, this way I can read a lot of papers about it and not feel bad that I’m wasting my time – I already wanted to read more about it anyway.
Skipping class was a bad idea
Unfortunately, I ended up deciding not to go to Dr. Conticello’s class, so I could continue sifting proposal stuff. Protein coronas are so cool, very complicated and there are thousands of questions to be asked – the problem is – they are ALL fascinating – which is unhelpful. I had serious issues narrowing things down. I’m still having issues with that. I felt as if class in the middle of the day completely broke my focus.
Also, I wanted to try to take the bio cume. I didn’t think if I took the bio cume and went to class I’d have enough time to finish my proposal AND the problem set from Dr. Weinert. I thought of it like a triage situation and decided to take the cume and skip class. Bad move. I regret it. It won't happen again. *sigh* Missing class is just wrong, no matter what the consequences, I decided. I don’t want to make a habit of it. I wish I didn't do stupid things, but there it is.
Keon texted me and was like, “Where are you? Is everything ok?” And I explained what I was doing. He was sweet and said he’d taken pictures of all the slides and I could look at them later. Dr. Conticello still hasn’t put anything up on Black Board.
I was in psychology all day, reading, sifting, and writing notes on that one awesome protein corona recent review I had, pulling references from it – it had great ones.
Wallace walked by and talked for a sec and we exchanged stories about how crazy things were. I told him I was in here and not in lab so I wouldn’t be tempted to do an experiment, and he laughed. I probably wouldn’t have been tempted at this point, but it was generally quieter in psychology.
Let me just say, I’m extremely amazed at the sheer number of esoteric instruments and techniques there are to measure tiny properties of molecules that I never even knew existed or heard of before. I’m continuously amazed by this fact. I found a lot of new ones in my sifting.
I ran into nice people unexpectedly
Unexpected thing #1
So, Thursday was kind of unusual in that I ran into nice people twice. I ended up going to Rise and Dine for lunch, because I’d only brought one sandwich and was feeling hungrier than that. I had French toast and a croissant – so good.
The waitress was pouring out some really good looking drink with whipped cream – I’ve seen them do this before – this time my curiosity got the better of me and I asked her what it was. She said hot chocolate. And I said, oh man! It looks SO GOOD!
She gave her hot chocolate to someone, came back, poured a little in a small cup, put whip cream on it, and gave it to me! She said, here, there was some leftover. (!) I was SO amazed and said THANK YOU!! That made my day – I was so, so happy. That was good hot chocolate too. I couldn’t have drunk much more than what she’d given me because I was too full anyway.
I felt like, the Lord must have blessed me extra. My mood went from neutral to really happy. I gave that waitress a stupidly good tip; I couldn’t help myself.
Unexpected thing #2
I was about to pack up for the cume around 5:30 p.m., still studying in psychology, when a random guy came up to me and said something like, “Hey, I don’t want to harass you or anything, but here [put a dollar by my laptop]. I know it’s not much, but go buy a treat for yourself or something. I’ve seen you here all day working so hard. Have a good weekend!” And promptly disappeared.
Once again, I was amazed. Nice people twice in one day?? When does that happen? A few I related that to doubted the sincerity of this person. I suppose I can understand that view, but he didn’t *look* insincere or suspicious in the slightest to me at the time. I decided, however he meant it, the Lord knew I wouldn’t take it negatively, and I felt as if it was just more bizarre encouragement from Him.
I was like, wow, I got hot chocolate and a dollar from the Lord today! He really *does* love me! This made me smile. I have no idea what I’m going to do with that dollar. I feel like it’s too special to use on me.
Dr. Conticello’s cume
I went to take the cume. While waiting for Dr. Conticello, I was still furiously writing ideas for my proposal. He came and slapped my notebook saying, “No more studying!” I realized, he probably thought I skipped his class to study for his cume. *sigh* I wish that were true.
I didn’t think I’d have much chance on it, really. I hadn’t studied at all – but I *really* wanted to see it! So I looked at it, reading all the questions, and took stock of the protein chemistry I need to know better. There’s a lot. About half of it was familiar or I felt that almost, I could do. But it wasn’t worth staying two hours for, when I had assignments due. So I left.
I was rather discouraged, coming home. I still couldn’t narrow my proposal topic down. And thinking about the cume, and all the papers I’d been sifting through, I was feeling overwhelmed and like, there is just utterly too much information to know. How am I going to learn and remember all this stuff, even in five years? There’s just too much of it. I'm not sure that's enough time.
So unfortunately, I had a nervous breakdown around 8:00 p.m. I was just so upset and mad at myself for putting myself into this situation. John asked me how I was and I burst into tears, saying hysterically I was a failure at life, I was pretty sure I was going to fail everything, there was no way I could learn everything, there was just too much information, I couldn't narrow my topic, I didn't know how I was going to get my HW set done, I was terrible student … [etc]. He just held me and said he was here for me and it was going to be ok. John is the very sweetest person I could ever have. He doesn't ever get upset with me for being hysterical. I also tend to be somewhat of a clingy person. But he doesn't mind this either.
Finishing my HW set
I calmed down and started working again, as if nothing had happened. I managed to *make* myself narrow my topic. But it’s not very good. I need to fix it.
I worked on my HW set then, typing it up and finishing the last two parts of problem 4 and all of problem 5 that we hadn't gotten to in group study. I knew it was going to be a long night. Sadly, it was. I’m glad to say though, I felt as if I answered all the questions satisfactorily. The last problem was a toughie – asked about the mechanism of the formation of a precursor molecule. I looked up stuff in my old orgo books and eventually figured it out – but I didn’t understand, at the time, why that reaction should work. It technically shouldn't.
I went to bed at 4:30 and got up around 6 a.m. I woke up and was like, “Ughhhh – oh yeah! It works because it's an enzyme reaction and the phosphates are being chelated by Mg2+! And I remembered I’d forgotten to remember assisting amino acids. So, I added those.”
And that was pretty much Th. I really don’t like all-nighters – I can’t really describe how much – but I was very happy that I did get a speck of sleep. So technically, it wasn't one.
Friday: a tiring, but interesting day
So, on Friday, I went to class and some of us students talked about the homework beforehand. I showed Gokul my proposal topic. He said it sounded pretty good, which I told him was comforting to me that he approved. He gave me this face like, “What, are you crazy?” His proposal got rejected twice he said, because other people were doing similar topics, and sounded terrible. I had heard about this – I felt really bad for him – I’d hate that to happen to me.
I told them about these neat enzyme articles I found, about how kcat/Km wasn’t a good comparator of enzyme efficiency between two enzymes on the same substrate, because that value was substrate dependent. It was a fascinating read. Gokul asked me how on earth I was always finding these good articles. I said, I wasn’t sure, except those I found on Kevin’s desktop – so I guess it was because the other grad students read cool stuff.
Bioorganic was very interesting
Class was fascinating – I really enjoyed the discussion of the homework – hearing what other people came up with and what Dr. Weinert’s comments were. Some people came up with some really interesting stuff. We didn’t get through the whole thing. She said she wasn’t going to grade it harshly – for which I am eternally grateful – because, there are no right answers, but she wanted us to think about it seriously and it was good for us to group think some of these things as well.
I told her to let me know if she had any comments on my proposal topic and it was too broad and I needed to work on it. She said that was what this month was for! She was very kind – and didn’t seem worried about it. I was so incredibly relieved.
Going to lab and talking to Kevin
I went to lab and started setting up an experiment – I was determined to do one – I really wanted to figure out this strange DNAzyme data.
I showed my data to Kevin and we talked a good while about it. He said he didn’t think the bands ran off the gel – I said, I know – it didn’t seem likely to me either, but if not that, then what happened? Look, they’re gone and then they reappeared! He was like – oh, that’s the same reaction? That *is* weird.
He had some really great ideas. First great idea was to use the RNA 10mer as a quick and dirty ladder of where a 10mer should be. Excellent. I should have thought of that.
Secondly, he looked up how long his DNAzyme reactions took to react. He said he never actually did 2 mM Mg2+, but it’s possible that the DNAzymes didn’t react even after overnight – they were just that slow – and it would be a good idea to see what 10 mM and 50 mM of Mg2+ could do. That made sense to me. I can’t remember the details. At the time, focusing was hard. But from looking at his data, that’s what he thought.
The math made no sense, but Kevin saved me again
So, I continued gathering things for the reaction and was looking over my math. I had everything prepped to pour a gel. Unfortunately, the math was making no sense. This greatly irritated me. It *should* make sense. So I went to Kevin again – and was like – Kevin – this math makes no sense. Can you look at it? He said sure! Kevin was so helpful on Friday, oh my goodness. I’m so glad he wasn’t busy.
He went over the math, we Nanodropped some things – and I figured out what I was doing wrong – I was confused at the time, about the total number of moles of FAM substrate I had. I was calculating that I could only do 20 reactions, with the amount of FAM 45mer I was using in each experiment – and I *knew* that was wrong. Yep. It seems I can actually do 200,000 reactions. That was very comforting. Somehow, I was mixing up molarity and moles, I think. And it seems as if my stocks are pretty accurate after all, so that’s good.
Slowing to a grinding halt, alas
Unfortunately, though, the longer I worked, the slower I got and the worse I felt. I wanted to get my reaction in before lunch, so I could image it at 6 p.m., but I ended up hitting an exponential curve of feeling worse and worse and moving increasingly slowly, at an exponential rate. I was like – I *will* do this reaction! I *will*! Maybe. Maybe, I will. Maybe … not. Maybe, not. ARggggg, come ON, go faster! *flop*
I gave up around 1:30 p.m. and ate lunch. Maybe if I’d eaten lunch at 11 a.m. I could have done it – I dunno. John called me about noon and told me to make sure I came home early, because even he was having to drink energy drinks. He hadn’t slept well at all without me in bed.
Ian had a good idea
So, I decided I would go home and sleep after all. Ian came and we discussed the experiments and I told him what Kevin had said – it was an interesting conversation – he said, he thought it would be good to setup a reaction like I had planned, but let it go over the weekend, so there would be no excuse for it not to work. I was like – yes! – that’s a good idea. I was so relieved – I didn’t want him to have nothing to do. But it really worked out perfectly. I had everything setup for the experiment so he just put it all together for me and I went home, around 2:30 p.m. ish.
I got home around 3:30 p.m.-ish and slept til 7:30 p.m. Then I ate some dinner and wrote for a while until John got home from Brian’s house. Thus ends the illustrious Friday!