1) finishing my rotation in the Salaita lab à moving to the Lynn lab next
2) performing my last experiment
3) giving my end of rotation presentation
4) some philosophical discussions and ...
5) the lots of silly stuff that happened in between
It’s true that I write too technically
Looking at my blog, I realize that I write in chemistry speak, and should be more explanatory about some of things I say – sorry about this! This blog is a work/experiment in progress. Eventually, I’ll figure out how it should be done.
Dad says I have too many cat photos on my blog – a humorous conversation
I was showing my parents some of the photos I put up here on the random section last week. My parents always forget what my website is called and how to get to it. "cu-lu-r-i-e-n ... whaaaaat? How do you spell that again?" My dad was like – “… is that ANOTHER picture of Camie? You just HAD one, previously! How many of those do you take!” I was like, “What? She was sleeping in a different POSITION!” He said, “Noooo, come on – it’s the SAME photo.” It was a very amusing conversation. I do take a lot of pictures of the cats, especially Camie, making cute poses on the clothes. I’ve missed a lot of opportunities to take even more due to not having a phone on me when I see her. So, if you think there are too many, like my dad, you can be glad that I don't always have my phone on me.
Expansions for blog in future: bios
I also told dad I’m planning to expand my “family” section with bios for all the immediate family, so he wrote me a partial one, that he had from his CV for work. I was very pleased. Eventually, these are going to go up there – but I want to post them all at once. I can write one for my brother pretty easily, but my parents, John’s parent’s and his brother are more challenging. My family are celebrities to me. They should have their own bios (300-500 words each, nothing serious). Maybe someday, I’ll expand to include grandparents.
Tuesday: feeling better and lots of grading student papers
I had largely recovered from the intense depression of Monday. I didn’t end up leaving until 9 p.m., because I was setting up my last experiment. I was thinking I could do the experiment Wed / Th, but I suddenly realized that I really needed the entirety of Thursday just to work on my presentation – otherwise, I’d have no peace. So I setup the experiment Tuesday night, into Wednesday morning/afternoon.
Wednesday: last experiment, discussion w/ Ian and Khalid
I woke up on the dot at 5:30 a.m., sprung out of bed and left for Emory, rather than moaning and rolling over, like I usually would. I’d showered the night before so that I could do this. I got there at 6:42 a.m., and after my usual routines, started my experiment. I was determined to get it done as early as possible so I’d have the most time to work on my presentation for Friday.
Weinert’s class: what happened to her office
Dr. Weinert came slightly late to class and said that she was sorry about that – her office was flooding and she had had to rescue her electronics and unplug her computer (!). My first thought was – oh no! Is it our fault? (When our lab defrosted one of our fridges, it apparently dripped into Dr. Dyer’s office below.) But of course not – her office isn’t below our lab. She said that she suspected it was the computational people above her. Our classmates and I looked at each other – Gokul and I said – what the heck are THEY doing that could flood her office? They don’t have fridges! … or DO they! Maybe they freeze things we don’t know about. Or maybe, they have large coolant vats for their computers. I have no idea.
Weinert’s class: getting our tests back
Dr. Weinert handed our tests back. I was planning not to look at it. I wanted to bury it. I told this to John and he pantomimed burying it for me in a way that made me laugh – he said – when you bury it, you HAVE to do it like this, with this kind of expression. It was hysterical. But I didn’t have a choice, I had to look at it, because she plopped them in front of us with the grade on top. Gokul said he could see me trembling and to calm down! I also hadn’t eaten anything. That didn’t help. It could have been worse. My score was below average.
However, to my compete amazement Dr. Weinert said that she was very impressed with ALL of our tests. I felt like saying: “[…] not with MINE you weren’t.” This was the best average she’d had: 136 out of 200. Mine was 119. There. I told you. Now you don’t have to wonder. Not acceptable. I don’t like to depend on curves. I’m going to do better. She said she’d give us twice as much time on the final for the same length of test – this made me feel better.
About the class
The class has been interesting lately. Flavins are actually pretty amazing – they can do 1 and 2 electron chemistry (radicals and non-radicals), as well as deprotonate a neutral amine on the ring, due to their unique resonance formations. It’s a beautiful molecule – it’s just perfectly designed to do what it needs to do – react with oxygen. I didn’t realize that oxygen was a diradical molecule and the only reason it doesn’t react and destroy everything around it is because it’s “spin forbidden.” I need to understand this better. I’m going to try to look this up later at some point.
After class, I at at Rise and Dine and got a latte. They made it BEAUTIFUL for me! I loved that.
I setup and was running my gel and Ian came by, the senior undergrad who is working on the project with me. We discussed my rotating out. I proposed to him that, although I was rotating out, if he wanted, I could still be involved in discussing experiments and designing them with him and what did he think about this? He said he would REALLY appreciate that. I was overjoyed to hear it. I thought it wouldn’t mind, but I didn’t want to assume. Also, Ian has dropped his advanced organic chemistry II course, so he’ll have a little more time for research, and can actually come in on a Thursday to run gels. For this work, you really need to come in back-to-back two days, to get things done. I wasn't sure how that would happen without me there, but now, it's all just worked out perfectly. It would have been hard before, since he could only do Wed/Fri, but now, he’s good for it.
He dropped the class – though Dr. McDonald said he had the highest average in it – because he completely hated it in every way, he said he didn’t need it for his degree, and whether or not he’d get an A in it was up in the air, the assignment grades were unpredictable, and the reactions they were learning had no rhyme or reason or pattern to them, so they were impossible to learn without memorizing each and every one separately. I discussed this with him before. I didn’t agree with his decision and tried to dissuade him. But, Ian does NOT like unpredictability. It seems built into his personality. I’m glad that he’s happier at least. He had to pick up a directed study course so he’d have enough hours.
I enjoy discussing science with Ian and this is why
I love hearing Ian’s ideas – he always thinks of things that I don’t. I really respect his opinion. I absolutely love the fact slap that he and I can get into – heatedly discussing science with him or experiments. It can sound like arguing – and I probably also have a serious/stubborn/determined face during these conversations, as does he, which makes it REALLY seem like arguing. But it’s really just interesting, stimulating conversation to me - an intense idea exchange. I love this kind of thing.
It’s hard to find people who can 1) engage in it about science 2) can “take it” and not think that I’m trying to refute them. The faster and harder the fact slap, the better. I’m not annoyed while discussing – that’s my focused look. It’s like a hand-slapping card game, but with facts. I’ll push Ian to explain his point, countering with some fact, and he’ll argue back, countering with a different fact – and we can get a good back and forth fact slap going.
It’s also an endeavor to understand the other person’s point-of-view. I WANT the other person to challenge me and defend themselves, to better understand why they think what they think. It ends once I understand the point and we either come to agreement or agree to disagree. Unlike what it might sound like, as I vigorously defend “my turf” of the fact slap, I have no attachment to my facts whatsoever and will immediately concede them upon proper evidence. I'm always so happy to find more people to discuss in this way with me. It’s extremely stimulating – one of my favorite things to do.
I’ll always feel someone out, to see how hard I can push them and/or, before engaging in one of these. This is not a type of conversation one has with strangers. One has to first see if they’re the kind of person who won’t be offended. Some people don’t like to be challenged or see hard-nosed fact pushing as a desire to show that they're wrong, which is never the case with me. It’s always a desire to understand the system better. Fortunately, I think Khalid is realizing this about me, so I’ve been able to discuss points more vigorously with him and have more fun.
Discussions with Khalid
Ian and I got to talk to Khalid about the experiments. It was great discussion. He wrote up a flow chart of the reactions on the board outside his office, which I suddenly realized that I needed in my presentation. It was perfect!
Yuan and Yvonne were eating more strange food. It looked like a brown nut. They asked if I wanted any and I said maybe, but when they took off the shell I said, “[…] EWWW! No, I can’t eat that. That’s gross.” It looked like an eyeball! They laughed and said oh, yeah, it was called “eye of the dragon” or something like that. They got it at the H-mart. Kevin asked if it was liche. I don't think it was.
Hmm. I just looked up what one of those looks like. I *think* I might have seen one at the farmer’s market! Nope. Must have been something else. I didn’t notice that it smelled badly. There a lot of strange, spiky fruits that get sold at places, it turns out. See photos below that I got off the web of what durian supposedly looks like. I'll have to ask Kevin or Khalid if that's actually the right fruit or not.
I saw Dr. Weinert coming into the building as I was leaving to image the gel in Rollins and she smiled at me! I thought that was nice. She’s such a serious person, she doesn’t always smile, though she’s very nice. Or maybe it was because I was walking down the hall at the time, saying “la la la.” It was kind of like: *distractedly, in a sing-song voice* “La la la la la la la la la la la la la la la la – oh hi! […] la la la la la la la la la la la la la la la la.”
So, I tried out the idea we had hoped would get our enzyme to ligate the splice product that we wanted, but it didn’t work, exactly. I think I’ll have to lower the concentration of the enzyme to the same level as the DNAzymes. It’s possible we might have gotten the right size band in the overnight reaction, but it was very faint. It’d probably be good to order a 25 bp DNA as a ladder marker control for it. I might suggest that to Ian.
Other photos from Wednesday
Thursday: working on the presentation
Discussion: literature and my experiments - random thoughts
It seems that Shuman, one of the researchers who has done a lot of work with my enzyme (rtcB), published a paper saying that rtcB absolutely REQUIRES having GTP to ligate 2’-3’-cylic phosphates with 5’-OH: something my experiment denies. RtcB in my case worked just fine without GTP. His experiments were at pH 8 – the only significant thing I can figure is different – and I’m wondering if that has something to do with it. I’d dearly love to know. Maybe Ian's experiments in future will shed some light.
I’m also wondering if that small species that we’re seeing that looks like a cyclic phosophate versus a linear phosphate could also be explained by a 1-2 nt difference in the substrate, if some of the RNA were getting hydrolyzed off the end … I’m not sure I could distinguish such small differences on the gels I’m running, however. Usually, to distinguish 1-2 nt differences, one needs to run the longer gels, like I ran in the Kushner lab or that they run in biochemistry, that allow for longer separations. This almost makes me think that that small species we’re seeing in something entirely different. I don’t know. I won’t be convinced until we run more experiments.
RtcB was only recently discovered – or relatively recently – so a lot about it is still unknown. It’s cool that I might have discovered something new about it. I’m just not sure, sometimes, that I can believe that. It must SURELY have another explanation. I dunno! I guess we’ll see. Ian and I will keep discussing this and potential experiments to run. I think we can come up with some cool ideas. Hopefully, Khalid doesn’t mind, if I still discuss experiment ideas with Ian. I don’t get the impression that he does. I’ll make sure it doesn’t absorb all my time.
What Ian did on Thursday
On Thursday, Ian came in and ran a gel and imaged it solo - he just asked me questions as needed. I forgot to remind him about a control lane - VERY unfortunate - but regardless, I think the gel suggested the longer DNAzymes seem to run at 37C. Now we have to see if they can do multiple turnovers.
Friday: presentation, feared meltdown that didn't come, and the Lord provided lots of things to comfort me
To me, the world ended at my presentation. When I have one of these to do, that’s all I can fit in my mind, and nothing exists after it, until it’s over. I was pretty stressed. Yvonne found me, asked how I was doing and gave me a nice, long hug and said, “Don’t be stressed!” I so appreciated it. I really, really needed it, at the time. I think the Lord sent her. He worked lots of things out in general, the whole week, so that I’d feel better. She said, she’d buy me coffee! And don’t stress. Just relax and breathe deeply.
I finished a few tweaks on my slides and went to our lab meeting room, and ran through it twice, so I’d have a general feel of what I was going to say. It took about two hours – from 11:30 – 1:30 p.m. This is absolutely necessary for me not to feel panicked about a presentation. I didn't get to do it for my Cas9 once - hence, I was very panicked.
Before and after running through this presentation, I was feeling almost like I might fall apart – I wasn’t sure, so I prayed about that, a lot, that somehow, the Lord would help me. I wasn’t sure exactly what to pray for. *hate on presentations*
I also had a lot of stress the whole week about leaving the Salaita lab. I can’t tell you, I can’t tell you, how much I dislike rotating out. It’s really stressful. It seems like a LONG time to me. Probably not many people understand this and just would find me odd. Well, I’m an odd person, it’s true. I love my lab family. They’re all a perfect fit for me. And I don’t want to leave them for any reason. I would do anything for them, both on principle and from the heart. Khalid is a big part of that equation. I never, ever expected to find any professor I was so thoroughly happy to work for, in my whole life. The Lord did it. It'd have been impossible otherwise. Maybe Khalid isn't the perfect professor for everyone - but he is for me. You can only find people like Ms. Harmon and Khalid a few rare times in one’s life. They don’t come around every day.
Now that I found this amazing person – I have absolutely no desire to leave – for any reason – under any circumstances – ever. Maybe this is unique to me, but the people are a lot more important to me than the science, the location, the area, the name or anything, really. I’ll give up whatever quite willingly to work for someone I love. And I have everything I need here. Cool science is always happening at Emory. What more could I want? I value Khalid a whole, whole, WHOLE ton more than a fancy piece of equipment I could maybe find someplace else, or a fancy named institution, like MIT (where all the people are thrown to the wolves and die of stress anyway, I hear). Emory is already plenty fancy. And we’re going to be making it fancier! You just wait. It’ll happen.
So, I was kind of feeling panicked about leaving, something like: *eyes grow wide at the prize I found* *clamps onto Khalid’s shoe like a gremlin or little kid with separation anxiety* MINE. I claim Dr. Salaita. I don’t want to leave! You can’t MAKE me! *rotations pull me away* *panicked face* noooooOOOOOOOOooOoOOoOOOOOOOoooooOoOOOOO!!! *unwilling detachment* *broken heart*
After practicing, I went back up to the lab and Yuan called me to ask where I was – Yvonne had coffee! I came in, and Yvonne said, there you are! And dragged me to her desk and gave me a latte and cookies. Yuan, Yvonne and Yue all surrounded me and said comforting things. I hugged them. I love them so much and told them so. I really appreciated all they did for me. They’re absolutely the sweetest people ever. They made me feel loved and so much better, about everything. I owe them a lot.
Yuan helped me figure out how to hook up the computer. Sadly, Kevin wasn’t able to get durian fruit, but maybe that’s good. It’d probably have been disgusting. But I would have loved to see Khalid’s face and I would have DIED LAUGHING, I tell you.
Yuan and Yvonne also gave me my name in pumpkins! – four small pumpkins that they’d written a letter of my name on. I was so incredibly honored – it was very appropriate for me! And it made me feel even more loved than their buying a latte. I’ll take them with me to the Lynn lab and put them on my desk and smile at them. It’ll make me feel comforted and less distressed – a little piece of home and my friends in my new place.
Photos - of the Jess pumpkins and Salaita lab at my talk - notice how Kornelia is almost always looking at me
The presentation went all right – I wasn’t very enthusiastic and I didn’t speak perfectly and I was nervous and could have explained things better – but overall, I think it was better than the first one I gave about Cas9, where I almost died of stress. I hope everyone wasn’t too bored. I was so grateful that Daniel risked rush hour traffic to attend – for some reason – his presence is very comforting to me. He’s a like a gigantic teddy bear. Don’t tell him I said that. He probably wouldn’t be offended though. He always has such interesting opinions and facts to point out. Khalid asked lots of questions and there was lots of good discussion. I hope I can remember all the points. I wrote some of them down afterward but I think I missed a couple. I should have been writing them down during the talk, but I forgot, because I was nervous.
After the presentation, good sum up of things
I intend to read those papers a lot more in-depth, if not now, when I come back – about rtcB and its mechanisms – it’s fascinating stuff. I got to discuss some of them with Khalid.
Fortunately, after the presentation, I didn’t have a meltdown like I feared. The Lord helped me a lot with everything just in general, exactly what I asked Him for. I just felt drained thoroughly and numb. I couldn’t really feel anything. I gave Khalid a hug finally, which I’m very glad about. It’s important. I would have regretted it otherwise – I dispense the most love to people in hugs – pent up love with no outlet is frustrating. And it’ll make the months I’m not in the lab slightly more bearable. He says that he hasn’t any problem with me joining, which is a relief. I didn’t have any reason to think otherwise, but I wanted to have officially asked about it and make sure I had everything worked out properly. After that conversation, I felt much better, more than usual. It was a good summing up of things, I think.
Philosophy about rotations, stress, but it'll all work out in the end
I feel like overall, rotations are good. It’s just not something I’m very happy about. It’s good I’m busy, so I don’t have much time to think about how much I’m missing everyone. I refuse to count down the days. No. If I do, they’ll go by so much slower. I’ll completely ignore them and focus on my work, and hopefully, the time will fly by. I feel as if the Lord will use it all for good, to teach me more things I need to know. That’s the impression I get from Him.
On Tuesday and this week, when I was praying about this and my stress over leaving, I felt as if the Lord said He was going to help me not to be so stressed and be comforted, and would help the time go by quickly. And when I joined, I wouldn't remember any of the stress, for all the happiness I'll have. He's probably right. Lord willing, I'll never leave again. You might think I'm joking. I'm SO not. But whatever the Lord works out, I'm sure will be wonderful.
Also, He seemed to say that He'd give me encouraging things to say to Khalid this week that I wouldn’t even know about, and not to be worried that I didn’t understand what He was doing at the moment, because it would all make sense later. He says that a lot. It’s starting to be true, about things He’s done before, so I have no doubt He’ll continue to be right. And you know, He did help me a lot this week, to be comforted and less stressed, in so many ways - not just Friday, but every day. It could have been so much worse. I’m very grateful to Him for this.
Rotations will also give me time to think about other research, learn other techniques and come at it all from different perspectives, as Khalid says, which is a very true. I’m looking forward to trying new things – even if I AM scared of rotating in the Scarborough lab, for my third rotation. They’re inorganic – scary, scary. I’ll just cling to Christian in there and hope he can keep me from death. He’s so nice. Marika is also nice. Yuan introduced me to a few of their other people a bunch of weeks ago, around the time Matt Francis was speaking.
I still intend to talk to Ian and eat lunches with the Salaita/Hill lab as often as possible. I refuse to completely disappear. OHHH no, that just will not happen. I don’t think I’ll be able to make it to all the Salaita lab meetings though, which crushes me, but it can’t be helped. If the Lynn lab meetings haven’t changed, they are at 5 p.m. on Wednesdays. Being up at Emory at night late three nights in a row I think would over-balance me and is at the point to where it might start killing me. John needs me at home in the evenings. I don’t like it when we don’t see much of each other for THREE days in a row. Two is bad enough. Not to mention studying time. That’s secondary.
Keon wanted to borrow a lab coat
After the presentation, Keon wanted to talk to me about borrowing a lab coat for the career fair he was hosting at his church – he just needed one for one day. Most of them were too small. But we found him one that was properly dirty. Kevin approved this and asked if he cared if it were dirty – he said absolutely not! He liked dirty lab coats. He didn’t get to where one as a computational person. I can’t imagine being a scientist without a lab coat. It’s like … being a fisherman without a fishing pole – I don’t know – it’s just out of place. It's always good to talk to Keon. He's a comforting person to talk to. I gave him a tour, since he was there. He liked my tour, said my desk and said everything in the lab was cool and laughed at the note on my bench.
I found Morgan, my classmate who is rotating in the Salaita lab next Monday, trading off with me. I’m bequeathing her my desk for now. And I introduced her to everyone in the lab, so she could get settled properly. It’s important. I also showed her around a few things. I asked her about her project and she explained to me what she’d been trying to do in the Dyer lab. They were trying to get carbon monoxide to bind to the active site of this enzyme (lactase dehydrogenase, I think), to use it as a reporter molecule for thermal fluctuations – but unfortunately, they were not able to get the CO to bind.
4th Friday - it was cold outside - but the pizza was good
The 4th Friday was outside – it was cold as crap – I couldn’t believe they put it outside! I’m not sure which is worse though – outside in the cold – or inside in the tiny room in A316 that’s too small and noisy. There was Papa John’s pizza! That was good. And the periodic table in cupcakes. They were celebrating Mole Day. I forgot all about Mole Day with the stress this week – how unfortunate!! I love celebrating Mole Day. Dr. Parker, my gen chem teacher, is to blame for that. I got to catch up talking to Matthew Jones, Robert, Haitou and a few others.
I drove to Bryan’s house, where John was doing the role-playing event with our Warmachine friends, and laid out on Bryan’s couch in a semiconscious state listening to them talk for two hours. That’s about all I had energy for. Then I went home. I was going to wait for John to come home before going to sleep, but I fell asleep by accident, with Spock curled up on me, purring.
Saturday: the Lord doing more good things and resting
I took a nap today, then drank coffee and had silk pie from O’Charlies and wrote this note. Mom and dad got home from visiting GranBobbe for her 80th birthday. I gave her Apple Butter, from Jaemore Farms – it’s one of the preserves I bought, but didn’t know who it was for. I think that one was for her.
I was going to try to work today, but I really needed one day to recuperate, before all hell breaks loose again. One day. Then I’ll go back to insanity. All the stress of the presentation, the late nights, and the stress of rotating out this week completely drained me – completely. I feel so much better having rested. And I have my “Jess pumpkins.” And lots of other things. Khalid’s willing to keep me around. I think everything will be ok. The Lord knows what He’s doing.
I’ll update more as I have time – probably – once a week is all I can do, until I get my NSF paper finished, another Weinert proposal draft done (due the 8th), the Conticello homework set done, the midterm done and figure out what I’m researching in the Lynn lab. But, you never know. I seem to find strange time to write short notes that I don’t expect. May you all have a blessed Halloween / All Hallow’s Eve week, with lots of the Lord’s peace!