Humpty Dumpty had a great fall.
All the king's horses and all the king's men
Couldn't put Humpty together again.
Research Update: Short and Sweet - DISASTER STRIKES
1) This week, I ran a third DNAzyme digestion, ligation reaction, reverse transcription and then PCR of the cDNA, to confirm whether or not I could get splice product. It looked very similar to the other two sets of ligations that I had done.
2) I labeled my RNA for the third time with 5-IAF (5-iodoacetamidofluorescein). Unfortunately, I made a critical mistake that I think killed it. I heated it for almost 40 minutes at 70 degrees Celsius instead of 5 min. I think it died right then. Unfortunately, as I didn't have other RNA to use really, I labeled it anyway. Some of it was labeled but most of it was degraded.
3) I did a DNAzyme digest on my new (mostly degraded) and previous FAM-labeled RNA. The gel I got was really messy, but I did get the approximate cleavage products that I was expecting.
4) Disaster strikes: AND THEN, the bottom fell out of everything, as I talked to Kevin about control experiments and met with Khalid. We made some important realizations. What were they?? Read on. Or, skip to the bottom. Ok, ok, I won't be mean - it seems I don't have splice product after all. I was doubting it for a while. It didn't add up. But the way the news fell was a particularly hard blow: a year of work felt canceled. But was it?
For Newcomers, Recap and News
Last Month
1. Post, possible splice product found
2. Post, science is frustrating sometimes, a lesson in being thoroughly stuck
3. Post, new research plan and Khalid's treat to Slice and Pint
News/Other
1. Post, Khalid and Meisa's new baby girl!
2. Post, stories/photos of Salaita Lab members and their projects
3. Post, common questions about the lab and grad school
The Story: A Week in the Life of a Grad Student
Monday: Before the Disaster, the Idea That Almost Was
However, upon further conversation with Khalid, I found that there was a hole in my design. After thinking more, I argued that it still might work, and Khalid said it was worth investigating, which was good to hear. Still, it's not as beast of an idea as I had hoped.
Tuesday: Dr. Weinert and Choosing a Committee
Meeting with Dr. Weinert
Unfortunately, I got attacked by stress. All the possibilities that Dr. Weinert spoke about seemed overwhelming to me. I couldn't think of them all at once. They also reminded me that I needed to look at my Emory email, which I hadn't opened in some time, and that I had to choose my committee!
Choosing a Committee: What That Means
Well, I Knew One Person I Wanted: Dr. Emily Weinert
After they mentioned it to me, I asked Dr. Weinert on the spot if she'd be on my committee, and she said yes. I really love her - she's the greatest. She's always so kind to me, gives great advice, asks great questions, and doesn't mind a bit telling you if you're wrong.
I needed to pick two more for a full committee. In the future, one of them will rotate off and Khalid will be swapped in. I was torn - Dr. Lynn, maybe Dr. Lutz and a new professor, Dr. Ahmed.
Option 1: Dr. Lynn
Dr. Lynn has some work related to mine and is nice, though a little scary to me still - I don't know why. When I'm being reasonable, he's not scary. But, I'm not always reasonable. I thought he'd make a great committee member. He always asks hard questions and tries to make people think, which I feel is important and would be good for me - help me grow. I thought he was my best #2 candidate.
I didn't want to chose Dr. Conticello, though I think he's awesome and a sweet person - I worked for him one summer as an undergrad. I thought he'd go too easy on me. He can be that way, sometimes. I talked to Dr. Lutz, but he said that he was about to leave for a month to Taiwan and Russia. I wanted to talk to him about my work before I asked him to be a committee member and judge his reaction - whether he seemed interested and would like to be on my committee. But since he was leaving and I couldn't talk to him, I crossed him off the list as well.
Dr. Eilef Ahmed has just come to Emory this summer, but her work looked interesting to me. She did research on cross-linked polymer nanoparticles, among other things, and a lot of ligand synthesis stuff that I didn't know as much about. The nanoparticles caught my eye. She used them against cancer in her postdoc work. I read the paper and it was pretty cool. Her particles don't collect very much in the liver and spleen like most do. I wonder why. I thought it might be nice to have both viewpoints: a bio person (Dr. Weinert), but also an organic/nanoparticle person to offer a different perspective.
What I Decided
I only looked at the professors from the biomolecular division. Other people are combining biomolecular professors from those of other sections, as appropriate for their projects.
Wednesday: Feeling Less Stressed and the Famous Kroger
On Wednesday, Keon, Morgan, Gokul and Wallace - four of my first year classmates that I am closest to - agreed to eat lunch together at the famous Kroger. Keon found this Kroger and discovered that they had a sit down diner with fresh food and it was DELICIOUS. It's now a hilarious joke with us. No one believes him at first when he says it's the best.
Well, we met AJ in the hall - a real character - and Gokul and Morgan showed up - I told AJ about the lunch - he invited people - I invited a few more - and we ended up with nine of us! We drove down in three separate cars. We laughed and had a riotously good time - talking about funny things in lab, our bosses and funny things they did or said, classes and committees. I told them we're going to have to do this again, before classes start. The date is set for August 27th, 7 pm, at Slice and Pint.
Nine of us first year classmates eating lunch at the Kroger
Thursday: Depressed about my Data, but Yuan is Cheery
Hanging out with Yuan: grad student mixer and dinner
After my bad gel, Yuan invited me to go to the grad student mixer, and I went, feeling glum. But I like when she invites me to things. Her laugh cheered me some. We went under the same umbrella - I didn't have one. Jeffrey, her high school mentoree, and Edward, Kevin's undgrad mentoree, also came and were under one umbrella. We got there but the food was eaten already. I got to see Sam Hong, from biochemistry, who I knew in organic chemistry at Oxford. I got to meet and talk to his wife, an environmental grad student, for a few minutes.
Yuan thinks Edward and Jeffrey are funny
Then, Yuan suggested we head back, because there was no food. So, I did. I didn't want her to leave without me. She laughed at Jeffrey and Edward not talking, in spite of the fact that they were under one umbrella walking together. Edward said he was conserving energy.
Elevator racing!
When we got back into the building, Richard (Yang's undergrad mentoree) and Yang were coming toward us walking down the hall. Edward promptly said - "Yang! You want to FIGHT?" For some reason, our two groups both dived for the elevators, each going in a different one, mashing the "close door" button and trying to race each other to see who would get to the fifth floor first.
Yuan stuck her umbrella out the door as it cracked open, to make sure we'd win. However, Edward assured us that yes, we would win, because our elevator was faster than theirs. He knew this. And he was right. There's was slightly slower. We had a lot of fun laughing about this race.
It's the simple joys in life that make it great.
Dinner at Chipotle
I ended up eating dinner with Yuan, Jeffrey and Richard at Chipotle. Yuan and I went a separate way than Edward and Jeffrey and once again, we tried to race each other to see which person's way was fastest. Yuan was sure hers was. But, we lost - they got there ahead of us. Yuan said it was because I walk slowly.
At Home, Computer Game
I went home, and decided to take my mind off work by finishing looting a cave in Skyrim (computer game, for ye non-nerds), and finding a dragon word of power. I also forged some daggers for practice in blacksmithing and rearranged my books and loot in my house.
Friday: Humpty Dumpty
I assembled, considered and thought about my data the rest of the afternoon, drawing up ideas and future plans. Talking it over with Khalid, we realized that it was possible for one of my primers to amplify the splint and make a product that was about the size of my "splice product," but shorter, as I was observing. I hadn't seen it when I was looking it over myself, because I was looking at the hybridization products the wrong way.
Since I wasn't forming the splice product, and the lanes for "no splint" and "no rtcB" are identical, among other things, Khalid said that the best thing to do at this point was to verify again that my rtcB was active, before moving on to anything else.
Reaction: oh no and numb despair
God Blog: Reflection and Realization
The Morning
Thinking back, it seems that the Lord prepared me for the bad news already. This morning, I gave up to Him my worries, stress and frustrations, asking that He'd give me His attitude toward my bad experiments and nothing working. I hadn't asked that of Him in a long time. I don't know why. But when I asked, He gave me more peace than I've had in a while and, especially after reading some in John 15, I had a whole new perspective of the day. A bad day became a good day.
What I Did After
That fact was challenged by the disaster. After the meeting, I packed up everything and left at once. I wanted to be alone to think. I got home and wiped out another cave of enemies in Skyrim and found two more dragon words of power. Then I went walking outside.
What I Had Hoped
I had really wanted to work as hard as possible this summer to try to get closer to real results, so that I would have good things to say in this year's NSF graduate research application - a grant graduate students can apply to for funding. I applied last year and didn't get in, but got high marks. The reviewers gave as their number one reason for me not being chosen that I didn't have a publication and hadn't presented at any conferences. This summer, I wanted to push toward something awesome. I thought I was getting somewhere, and yet now, all that work just didn't seem to matter.
What I Now Know
While walking, I realized something important. I had been trying to make things happen myself, thinking that if I worked hard enough, *I* could get somewhere, by my MIGHT and SMARTS! Not exactly - but more or less. I realized then, it's not true. My might and smarts can't do anything. I also daily realize that I barely understand what I am doing and am not really qualified in the first place. Everything I do have and every good thing I ever get is from the Lord, not me. He gives me good results, in His time, His way. I can't will them into being.
James 1:17, "Every good gift and every perfect gift is from above, and comes down from the Father of lights, with whom there is no variation or shadow of turning."
Response and Thoughts for the Future
I decided, maybe it'll go faster this next time, since I've done it before. This is a good opportunity for me to re-think everything and make my project TWICE AS GOOD! Of course, I do also have to face the worst. Will I let data rule my happiness? That is the question.
While I was praying about it, since the worst had happened, all the other possible bad outcomes flashed before my mind ...
1. Having the project dead-end, unable to go forward
2. Getting scooped
3. Getting nothing publishable for five years
Anything could happen. I decided that it was important that I surrender to the Lord my own efforts - that I would work as hard as I could - but leave the results up to Him and be happy and content even if I get nothing to show for it. It's not up to me. He showed His sovereignty over me in this way. Looking back on how I was doing things, I think it's a lesson I needed to learn.
Therefore, I relinquished to Him my "right" to success, and told Him that He did not have to give that to me. He's the Lord. And I will trust His judgment. And I asked that I always enjoy research and always be happy, even if I never publish anything, things never work, I never get data, and the project dead-ends, and nothing ever works in my whole career. With this blow to my pride and losing a year, I felt like, I could finally relinquish that to Him in some small way - at least my project - something I've not been able to do before. He gave me a lot of peace. After I had prayed and walked, if I wasn't still totally happy, I felt as if the world was centered again, content and I could go on to ...
Attack the next question!
Conclusion: Onward and UPWARD!
Am I going to say that a year of work was canceled? Nah. It's merely another road bump. I just haven't found anything *yet.* That doesn't mean I won't eventually. In that sense, nothing has really changed!
Now, to answer the question: ARE you, oh rtcB of fickleness, truly active? Or are you just wiggling your fingers at me and sticking out your tongue? I might have to re-isolate you. OR, find another species of you that works better. I've considered switching variants.
Pictures from the Week
FIN: Appendix of Songs
Theme Verses
Habakkuk 3:17-19
Though the fig tree may not blossom,
Nor fruit be on the vines;
Though the labor of the olive may fail,
And the fields yield no food;
Though the flock may be cut off from the fold,
And there be no herd in the stalls--
18 Yet I will rejoice in the Lord,
I will joy in the God of my salvation.
19 The Lord God is my strength;
He will make my feet like deer’s feet,
And He will make me walk on my high hills.
"You Are" by Colton Dixon
Lyrics
When I can't find the words
To say how much it hurts
You are the healing in my heart
When all that I can see
Are broken memories
You are the light that's in the dark
You are the song
You are the song I'm singing
You are the air
You are the air I breathe in
You are the hope
You are the hope I'm needin'
Whoa
You are
And when my circumstance
Leaves me with empty hands
You're the provider of my needs
When all my dirtiness
Has left me helpless
You are the rain that washes me
You are the song
You are the song I'm singing
You are the air
You are the air I breathe in
You are the hope
You are the hope I'm needin'
Whoa
(Whoa)
You are the song
You are the song I'm singing
You are the air
You are the air I breathe in
You are the hope
You are the hope I'm needin'
Whoa
If I had no voice, if I had no tongue
I would dance for You like the rising sun
And when that day comes and I see Your face
I will shout Your endless, glorious praise
If I had no voice, if I had no tongue
I would dance for You like the rising sun
And when that day comes and I see Your face
I will shout Your endless, glorious praise
You are the song
You are the song I'm singing
You are the air
You are the air I breathe in
You are the hope
You are the hope I'm needin'
Whoa
(Whoa)
You are the song
(You are the song
You are the song I'm singing)
You are the air
(You are the air
You are the air I breathe in)
You are hope
(You are the hope
You are the hope I'm needin')
I'm singin' whoa
"You Are I Am" by Mercy Me
Lyrics
I've been the one to shake with fear
And wonder if You're even here
I've been the one to doubt Your love
I've told myself You're not enough
I've been the one to try and say
I'll overcome by my own shame
I've been the one to fall apart
And start to question who You are
You're the one who conquers giants
You're the one who calls out kings
You shut the mouths of lions
You tell the dead to breathe
You're the one who walks through fire
You take the orphan's hand
You are the one Messiah
You are I am
You are I am
I've been the one held down in chains
Beneath the weight of all my shame
I've been the one to believe
That where I am You cannot reach
You're the one who conquers giants
You're the one who calls out kings
You shut the mouths of lions
You tell the dead to breathe
You're the one who walks through fire
You take the orphan's hand
You are the one Messiah
You are I am
You are I am
The veil is torn
And now I live with the Spirit inside
The same one, the very same one
Who brought the Son back to life
Hallelujah, He lives in me
Hallelujah, He lives in me
Hallelujah, He lives in me
Hallelujah, He lives in me
You're the one who conquers giants
You're the one who calls out kings
You shut the mouths of lions
You tell the dead to breathe
You're the one who walks through fire
You take the orphan's hand
You are the one Messiah
You are I am
You are I am