jkirzner

I am a scientist

2008-01-11T01:39:05Z

Work has been very good now that my coworkers and I have been working really hard and I am learning new things. There was a period where we started a new project (no more cigarette smoke), and all I could do was shadow my boss and watch him do mouse surgeries, mouse dissections, and the benchtop work involved in analyzing tissue derived from these mice, feeling naive and confused. Now that I have learned more about what to do and written down the protocols, I have transitioned to actually participating, and it feels much better! A lot of it is memory, and muscle memory. It's one thing to try the first time to do a dexterity-intensive procedure, using foreign tools and not knowing how things are supposed to be and look. There was a lot of unsteadiness and indelicate movements and moving things back and forth to no avail, until eventually I got the hang of several procedures. There is room for improvement.

Things I have done in the last few weeks:

Shadowed my boss during a T cell transfer: This involves grinding spleens from mice with a mutation such that they have only one kind of T cell, then destroying the red blood cells, using magnetic beads to capture the cells we don't want in a magnet, and keeping the T cells that are left. We inject these T cells in the tail vein of mice with no immune system, so we know whatever effect on arterial plaque we observe is from those cells. We also injured these animals in their carotid arteries (see below)

Arterial injuries: I am a mouse surgeon! I have done several of these largely by myself, including practice mice and my very first mice this week that were part of an experiment. First we weigh the mice to determine how much anesthesia to give them, and then give them sleeping gas in a chamber so that we can handle them more easily to inject stronger anesthesia. My boss miscalculated and we lost several mice to anesthesia overdose. We shave the fur off their neck, and then cut their necks open and pull the muscle apart with two fancy tweezers to isolate the carotid artery right next to the trachea. We put sutures under the artery so we can pull on it to then put a plastic cuff around it. The cuff has a slit in it to slide the artery in. I made the cuffs myself out of plastic tubing I cut longitudinally, then cut the ends 2.5mm long, and made two slits in it that we put sutures in so that was can tie the cuff closed so it stays in place. I learned how to make surgical knots. I also learned how to tie stitches when we close the wound off. The delicate stuff is done under a dissecting microscope because mice are very small. I am proud to say that I have learned a lot about what to do and how to maneuver things, and my hands have learned more about what to do. I will get even better with time. The whole point of the cuff is that it accelerates the hardening of the artery, so we can more easily study what is involved in accelerated plaque formation and the thickening of the arterial wall. The immune system is involved in this process, and that is why we study the spleen, because that's where a lot of immune cells hang out, even ones invovled in the arteries.

FACS (florescence-activated cells scan) analysis: This involves isolating cells and staining them with colored antibodies or other colored chemicals specific for whatever you are studying. The FACS machine analyzes a liquid you give it, containing cells, by using what I'm told is ink-jet technology to run one cell through the detector at a time, shooting a laser or something at it to analyze the intensity of the color you have stained it for. If the cells are concentrated, you can look at 10,000 in 5 seconds. Each cell is a separate data point, so when you stain for two things you can tell how many of the cells are strong for A and strong for B, strong for A and weak for B, weak for A and strong for B, or weak for A and weak for B. It is on a continuum so you can have any combination of cell subpopulations of intermediate intensities. We've been looking for molecules that show up on CD8 T cells' surface when they are activated or become memory cells, etc. Today I used the magnetic beads to isolate T cells from an injured mouse's spleen, and I am staining it overnigth for FACS analysis tomorrow. I have done FACS before, and I am familiar with the software used to make sense of all the datapoints.

Skills I have yet to learn: Sectioning. Sectioning is when you imbed, say, an injured carotid artery, in a freezing goop that solidifies when you freeze it on dry ice to make a solid block that can be sliced in a refridgerated cryostat machine. These slices are put on a microscope slide and analyzed in several ways. You can look at the cross section of the artery to measure plaque formation. I have experience staining these slides for several targets using antibodies (Immunohistochemistry), or with just color stains used to measure the area. I have expreince analyzing the plaque area or stain area on software on a computer attached to a microscope. I have not done the sectioning myself though, and that is something else to learn. It's delicate but not particularly complicated.

My boss is a little insensitive, but he's a good guy. Things are complicated, and sometimes I repeat my questions, but he doesn't always just answer my questions, sometimes he tells me I should know. I'd imagine the environment would be probably more unfriendly in the biotech pharmaceutical industry. We have both been working very hard lately.

I am way behind on reading other peoples' livejournal posts. Oh well. My busy-ness is a product of my life being interesting lately.

A lot of this stuff is hard work, and I feel like I have it in me. I understand that the reason so many people here can't speak decent english is that they know how to do these procedures well, and that is what is most important. Hopefully I can be as productive as they are.

LA Times Journalist Makes no Sense regarding Amgen Technology

2007-08-16T00:10:06Z

Apparently Amgen has suffered some setbacks, inspiring this journalist to say something that doesn't really make any sense.

http://www.latimes.com/business/la-fi-amgen9aug09,1,1332567.story

"Founded in 1980 as AMGen (Applied Molecular Genetics), the company pioneered products based on advances in molecular biology that have enabled scientists to use living organisms manufactured inside living cells to create novel medicines."

I don't know much about Amgen, so I guess he is referring to recombinant expression technologies, where cells or bacteria are used to churn out proteins, and decided to throw in random words.

Finished a presentation

2007-08-03T22:06:57Z

I just presented my data at an Atherosclerotic Research Center informal meeting. It took about 15 minutes and was in front of like 25 people including a bunch of MDs and PhDs and MD PhDs. When I first started studying and practicing, I had a bout of "I'm stupid and I can't do this well." Now I feel accomplished and empowered. Back to work!

jkirzner @ 2007-06-11T13:15:00

2007-06-11T20:16:27Z

My car died. It's in the shop. I'm using my mom's car. I don't know what's wrong or how much. It was chugging and not responding or engaging after pressing the peddle. The problem manifested itself on and off in between actually engaging. It's probably something with the transmission. I might buy my mom's car from her if necessary. I have a lot of money in the bank from not paying rent.

I had another instance of my recurring dream where my teeth fall out. It sucks until I wake up and realize it's not real.

jkirzner @ 2007-06-02T21:13:00

2007-06-03T04:17:22Z

A. Finished online traffic school! Woo hoo! I read all the lessons and it took me seven and a half hours with short breaks. Thanks to madbard for discussing the idea of copying all the lessons into a word document and then using the find tool to search for the answers to the questions.

B. Work is good. My boss figured out something we were doing wrong and now the rezultz are wicked good. We submitted an abstract for the American Heart Association meeting. Boss said that 75% aren't accepted.

A big loss

2007-04-03T22:35:19Z

In the vivarium, where they keep the animals, some animal handler knocked over lots of our cages and the mice got out and were irrevocably mixed up. My coworkers lost thousands of dollars and months worth of work. The handler was working with bad vision or something. He was fired.

Contractions (of language, not of uterus)

2007-03-27T17:33:04Z

There's a hip hop song I hear on the radio that has these lines:
You ain't
'cause you not

Which is a way of saying:
You aren't
because you're not

Which are two ways of contracting the same thing:
You are not
because you are not.

This common identical soure of two different contractions pleases me.

jkirzner @ 2006-08-21T19:52:00

2006-08-22T02:53:52Z

Gone to visit relatives and Shlomo in Michigan tomorrow until the 30th. I'll also get to see Shlaura/Laurmo (schweet!). After I come back I start my job search.

Scissor Sisters: Awesome Music Video

2006-08-09T21:36:58Z

Highly recommended: super-glam funky music by the Scissor Sisters called "I don't feel like dancing". It's really gay and really awesome. You can search for the video on launch.yahoo.com if you have a yahoo account.

Poker, Disneyland, Thesis

2006-02-14T02:35:28Z

On Friday I bought in for a $10 cash poker game and came home with $59. I could not lose. We were playing pot-limit and I kept betting the pot. Not once did I stone-cold bluff - I had a piece of every hand I was in, usually at least top pair. I got lucky and I didn't back down to people trying to scare me away.

On Sunday I went to Disneyland with Josh and Tim and his girlfriend Kate. I got up at 7:30am and left the house at 8:00 and came home by 4:30pm and didn't have any problems except for a headache. It was a lot of fun. The Indiana Jones ride was my favorite. I parlayed the early rise on sunday to going to bed early and getting a reasonable rise today. Hopefully I can get up earlier tomorrow.

I have started writing my thesis. I have an outline. I am starting off with background/introduction, so this involves looking at papers and summarizing what is known already by other people about what I am studying. It's going to happen. If I can't finish by mid May (about 3 weeks of being finished in advance is required for submitting it to my prof for editing and to my committe for reviewing), I will postpone and finish by the end of summer. There is still more experimentation to do, but I am working on the Intro now. I am done with my classes.

Wasted my day

2006-02-07T06:07:29Z

I totally wasted my work day today farting around and sleeping in the library. Then I went home to work at home and I don't have remote access to the library's journal database, I guess because I'm not paying for my tuition because I'm not taking any classes (all done). The paperwork to pay a dummy $187 to be technically enrolled so I can graduate hasn't gone through. My only choice is to vindicate myself tomorrow by getting up early. I hope I can do it. Here's wishing myself good luck.

Karaoke

2006-01-09T22:48:04Z

Did karaoke for the first time ever, with John Tchoe at Boardwalk 11. American Girl by Tom Petty went well, Lanslide by Fleetwood Mac didn't go well, and Brown-eyed Girl by Van Morrisson went well. People were dancing during Brown-eyed Girl.

John did a vulgar Adam Sandler song. I was uncomfortable but in the end everything was fine.

Earthsea and Automobiles

2005-12-30T01:29:07Z

I watched Earthsea on Netflix. It was 2hrs45mins long. Pretty good. It was like a cheap version of Lord of the Rings with some Star Wars dark side homages. It's possible to have villiany without challenging the protagonist to curb their anger and let go of their hatred, but the author felt compelled to put that in. The rest of it was pretty original. Not as much overt sorcery as I expected.

My car died on the freeway. I was scared until I got off to the side. I don't always have a cell phone so it's good I did. It's also good my car died when the traffic was slow, so that I didn't get rear-ended. It's 11 years old. I'll probably get a new one with the help of my parents. I told them I'm fine with a cheap-ass economy car but they don't consider small cars safe.

Poker

2005-12-18T10:50:03Z

Tonight I came in 4th out of 15 or so people at a poker tournament. I turned a $21 buy-in into $39, netting $18 and some fun.

The Light at the End of the Tunnel

2005-12-17T02:56:56Z

I will be presenting my research in the form of a poster at the CSUPERB California State University Biotech symposium starting January 13 in San Jose. I am so stoked. They pay for hotel, meals, and airfare. My supervisor is in India so I will be designing the poster independently. This is not a problem, merely a challenge. This is gonna feel really good. Last year's symposium was a blast.

Remember all the time I spent saying that I had no data? Well things have fallen into place and now I have data for three different types of experiments. I am on track to graduate in May 2006, and will be talking to the HR people at the convention and handing out resumes and cover letters for employment upon graduation. Also, I am the second author on a manuscript that we have submitted for publication in the journal Apoptosis. Our prior electronic submission to another journal was sent back within 24 hours of its submission. That's the way things go. This winter I am responsible for helping out another grad student and an undergrad. Somewhere along the way I became someone who knows how things work, don't ask me how.

After CSUPERB comes starting to write my thesis. I have made long presentations in three seminar classes, and I know this is doable. I really like the professors on my thesis committee. One taught a bioinformatics class with lab, and another taught a recombinant DNA techniques class with lab, and then there is Dr. Medh, my advisor.

Yesterday I went to a fun lunch at Acapulco with the people in my genetics seminar and didn't start in lab until 3:30pm. I ended up staying till 9:00. This morning I got up at 7:00 to take some samples to an instrument at UCLA. Things went well. Tonight I go to a CSUN party at someone's house. I don't quite work as many hours as someone with a full-time job or a PhD student, but I think, for that very reason, that this has been a good transition.

jkirzner @ 2005-11-13T19:21:00

2005-11-14T03:21:38Z

-Yesterday was the last homegame of the year for UCLA football. I have been working a lot of the games as an usher with Josh as my supervisor. It was nice to earn a little money, and in a few of the games my shift ended at the beginning of the 4th quarter so I could turn around and watch the field and enjoy the game after.

-My parents gave me $100 for my birthday. I don't usually buy myself too many things, so this was a good gift. I spent $30 on magic:the gathering online cards and have been playing that a lot. My cards are good, but some of the strangers I play just out-class me. It's fun to play against alphamonkey.

-uclafalcon got me a month of netflix for my birthday. I have seen Neverwhere: Disc 1 and 2 and it was neat to see the miniseries after reading the book. If I renew it, it will probably be the cheaper plan.

Transfected!

2005-11-09T01:11:29Z

My research took a step forward today!

I previously spent a long time amplifying, isolating, verifying, purifying and linearizing some DNA before I zapped some cells with electricity to comprimise the integrity of their membranes so they would take the DNA up permanently for the purpose of further experimentation. (This is called transfection and the method is electroporation). Then I treated them with antibiotics to select for the ones that had taken up the DNA (they were given antibiotic resistance for this purpospe) and spent a few weeks nurturing the few cells that survived the process, never knowing if it actually worked. The artificial DNA construct has a reporter gene (luciferase) that produces a protein which emits light at a certain wavelength in the presence of a certain chemical. Today I checked for the presence of luciferase and it turns out that the cells that really matter took up the DNA and I can procede to harrass them with various drugs and see how the reporter gene, which has an experimental regulatory region, responds!

... and this is on top of the successful Friday I had working on a separate project.

Reading

2005-11-08T02:20:37Z

I just finished reading "Persepolis : The Story of a Childhood" and "Persepolis 2: The Story of a Return" by Marjane Satrapi. They are black-and-white graphic novels about a Persian woman's experience in Iran and elsewhere. I liked them a lot. They're easy reads, but serious. The story is personal and interesting. I recommend it.

A Milestone

2005-10-27T04:30:50Z

Today I did a 1 hour, 15 minute presentation on Molecular Diagnostics in Forensics and Medicine. It went very well and was well-recieved. It was the last classroom assignment of my career at CSUN. I worked on it for a week and a half and it's nice to be able to relax and watch TV without jumping back to the project.

I feel I am a good presenter because I explain things in a conversational manner rather than just reading off the slides exclusively.

Now I can focus on more research, writing my thesis, and doing various other research-oriented presentations.

Jewfro

2005-10-02T01:00:08Z

I cut my Jewfro off. No more curls. Short and conservative.

Poker

2005-09-30T05:49:01Z

Today I played two zero-stakes no limit hold 'em tournaments.

At CSUN, I went all in pre-flop with AJ suited against A8. I lost when my opponent drew an 8.

At Yankee Doodle sponsored by PartyPoker.com, I had pocket kings in my last hand. A girl went all in with a small stack and two low cards like 79. Then I also went all in with this other guy to make a side pot. He had K9. She ended up getting a straight and he got three 9s.

Validation, Zero-Stakes Poker

2005-09-29T22:27:08Z

I started an informational experiment on Monday that requires me to make measurements each day and compare the progress. After today it was conclusive: the cells into which I put an artifical gene (for later experimentation) still maintained their usual respective sensitivity or resistance to a drug we normally treat them with. Implications: I almost certainly did not fuck up and accidentally switch tubes as I have been worried about neurotically. There is a chance that I mixed up samples within categories which behave similarly, but I don't think that happened.

Someone I know gave me the following analogy to apply to my research: when you are driving a car, you don't remember every turn you make en route to a destination, even though you know you are making the correct turn at any given stage, because you are aware enough of what you are doing at that particular point, even if you don't remember each step at the end. (I put everything in my lab notebook, but that doesn't help as far as mixing stuff up goes.)

On another note, there is a zero-stakes poker tournament on campus in a half hour sponsored by the school. Because there is no money involved, people will be playing weird. I will make adjustments. I will be tight, and I won't slowplay a good hand, because people will call with crap.

Procrastination

2005-09-26T22:29:51Z

Today was one of my worst procrastinating days in a long time. I got to lab at like 3:00. Now I am waiting for someone to be done with the sterile hood, but I WILL get stuff done today.

Double Dreams

2005-09-22T07:05:59Z

I don’t know if it was yesterday or today but I have this reoccurring dream about being in an English class and not doing any of the reading, even from the beginning, and then being faced with the assignment to write an in-class essay about the reading and being clueless and coming to terms with the probability that I would flunk the class. It was very stressful and shameful and I thought it was real when I was dreaming
jdkirzner: Then, I went back to sleep, and I had the same dream again, and I was convinced it was real again, even after the first dream, and I had the same depression and shame as the first dream.

Last Weekend

2005-09-21T20:14:39Z

Last weekend was busy and fun. Twice I got up earlier than I do during the week.

Friday:
Found $60 on the ground near the gym, split with Josh. Beat Josh at squash. Netted $24 playing poker.

Saturday:
Got up early and worked the UCLA Football game as an usher at the Rose Bowl. Mostly checked tickets at the entrance to the section. Josh was 1 section over.
Night: Went to Jennifer Hedger's party at her house. She works in the lab across the hall. Mostly hung out with people from that lab.

Sunday:
Got up early and drove with Jason, Sarah, Skan, and Steve to Nelson's wedding in La Jolla, where we met up with others. An awesome good time.

This weekend was pretty great.