[Most Recent Entries]
Below are the 4 most recent journal entries recorded in
|Monday, May 2nd, 2005|
|As the dead crow flies
My last two days of Pesach were much much more successful than my first two. I went with Jenny's family to their vacation house on Block Island. I love Block Island. I spent many happy summer days there as a toddler. It always disturbs me to have to sleep on land there, but it is worth it to get to visit.
One of the best things about the trip was the Grandmas. I've only ever had one grandmother, and she was sick. These Grandmas are in fine form, and the play off each other for endless entertainment. Grandma Goldie has silver hair and Grandma Sylvia has gold hair, so it's easy to keep everyone straight. Grandma Goldie is approximately 3 feet tall, and she has an adorable little granny haircut of bright white hair. Grandma Sylvia is bigger and has sort of orange hair, which sometimes matches her lipstick. They are both from Brooklyn, but now one lives in Florida. I think they must have known each other a long time - my impression is that Jenny's parents were dating in high school, so maybe the Grandmas have been hanging out since then. They love to reminisce about old times, and also comment on the present. The ages at which girls these days get married, for instance. Or what Grandma Goldie's father liked to do for Pesach. Or what Jenny was like as a child, or what her parents were like as children. I heard about all the cousins and aunts and uncles and distant relatives. The Grandmas engage in parallel story telling. It's much like toddlers engage in parellel play. They are aware of the other person, but aren't quite interactive. Rather they each take turns telling part of a story. They wait patiently for the other person to tell part of a story, and they continue with theirs. It can be a bit hard to follow, but it's worth it.
In addition to the Grandmas, there were Jenny, Karolina, Jenny's brother Simon, and Jenny's parents. Also Jakie, an extremely elderly dog. He is well loved, perhaps too well loved, by the whole family. Jakie appears to be approximately a bazillion years old, in dog years.
Initiation into Jenny's family can be rough. Last time I was forced to identify rice in its natural habitat. As in, the father comes in and says, "You're a biologist! I need you to identify this grub for me." Despite my assurances that I don't know one grub from another, I was dragged outside to the lawn to stare at small white grubby things. They indeed seemed to have colonized this part of the lawn. I was not the first person to have been drafted for this job, because there were a number of other opinions already gathered about the grubs. Apparently they hadn't previously been seen on the island, and there was some concern about new insect invasions. We all squatted there on the lawn, squinting at the grubs, when someone mentioned how they sort of looked like rice. At that point the mother starts yelling and gesturing, and explains how she had burned the rice and had thrown it out in the yard. Mystery solved and insect crisis averted.
That was last time; this initiation was entirely different. Upon arrival I am informed that I am needed for a task. Karolina and I both respond that we'd be happy to help, assuming we would sweep the room or set the table or do other normal guest coming before a meal sort of activities. But no. Apparently the task involves a dead crow. It is explained that a crow has gone and died in the bathroom and needs to be removed. At this point I asked, as anyone might, how a dead crow had come to be in the bathroom in the first place. At this point Jenny's father (Arlen) looks at me as if I lack some basic intelligence and says, "I don't know. Either it died and fell in, or else it was already sitting there and had a heart attack or something." Ah, right. With the situation now being properly clarified, we all trooped out to find the dead crow. It was decided the best plan of attack was to maneuver the crow carcass onto a shovel, carry the shovel into the bracken maze that extends from the backyard down to the sea, and pitch the crow somewhere deep in the thistles where Jakie wouldn't be able to get to it. Since Karolina is a squeamish vegetarian, I did all the action on this. She just provided moral support. It was as we went to retrieve the crow that I finally realized the bathroom was an outdoor shower, which at least cleared up some of the confusion. It turns out convincing a dead crow to hang out on your shovel is not as easy as one might think. The head is the heaviest part, but it was that part that was farthest in the shower, and so the last part to fit on the shovel. It took multiple attempts to finally get it. At this point the crow had a broken neck, but whether that was the cause of death or simply the aftereffects of the shovel is not known. We considered autopsying the crow, but decided against it. You will all be happy to know that I did an excellent pitching job and we did not see any crow remains the rest of the time we were there. I also felt that having disposed of the dead crow I didn't have to feel bad for not jumping up to clear the table with enough alacrity, or whatever other guest faux pas I might have made.
There is more, much more, to be said about this trip, but it will have to wait for a second installment.
|Tuesday, April 19th, 2005|
|looking out my back door
Sneaker count: 168
Today I sat on my front stoop. Growing up, I didn't know people had front stoops anymore. I envisioned sitting on front stoops as part of the days when all the Jews lived in Brooklyn, the tenements had no air, and the boys played stickball in the street and tried to get up the courage to ask the girls out for cream sodas. Alternatively, people in the south sat out on their front stoop while swatting gently at gnats and sipping sweetened ice tea or lemonade.
It isn't true, however. In fact, my neighborhood sits out on their stoops. It's great. I never really sit on my stoop, except times like today, when due to some crossed wires I was waiting for a ride that was never going to come. It was a great experience. First there was the three year old who was flirting with me from across the street. She was standing in her window. Whenever I looked at her directly, she stared through me as if I weren't there. But if my attention wandered, she would yell, "Hi! Hi! Hi!" until I looked back, at which point she would again pretend there was no one there at all. She was also distracted by whatever activity was going on in her own apartment, and so her head would swing back and forth, and all her little braids would swing around.
Then this guy drove past. He was what could only be described as a dawg. He was black and had cornrows and was sitting so far back he was practically in the back seat. He had his arms at full extension, and he was slouched down so far I don't think he could actually see over the steering wheel. He also was blasting rap and was grooving to the beat in a chill, I am so cool sort of way. What made this all so picturesque is he was driving... an Oldsmobile. Not a new one, either. Your parents' Oldsmobile.
Then the goth couple came home next door. The girl looked really good. She was tall and thin, all in black, with a short skirt that together with the tall platform boots showed off her legs very nicely. Her boyfriend couldn't really match up, but he did look very happy. It reminded me of a friend of mine. She is not goth, but I begin to think maybe she should be. This girl was hot, but I think my friend would look even better. She has the build for it, and the coloring, and her hair is perfect, long and straightish and black. I was sitting there, feeling the cool breeze, drinking in the new scent of cherry blossoms mixed with gasoline, and wondering when my flirt from across the street would return to her window.
Unfortunately, eventually I realized my ride either wasn't coming or had had an accident, so I had to retreat from my stoop and return to my daily life. But it was a nice break. Current Mood: calm
|Sunday, October 3rd, 2004|
|Saturday, July 17th, 2004|
Ok - all you math folks, this is the data problem I've been obsessing about. I need help.
I run these experiments. What exactly they are isn't all that important, but here is the data breakdown.
For each sample I get two results - one firefly and one sea pansy. (those are the animals we got the enzymes from - they glow in the dark!)
Let me think of the best way to explain this. Here is how I think of it. I have a cell - it has a firefly thingie in it that makes it glow. I am sticking something else in it - shRNA, to be precise, trying to make it not glow. So the basic experiment would be, take a cell without shRNA, check how much it glows. Call this C, for control. Then, take a cell with shRNA, and check how much it glows. Call this E for experiment. I have a luminometer to quantify glowiness.
E/C should tell you the percentage of glow the cell with shRNA has compared to the cell without shRNA. Very easy. (This glow is referring to firefly glow.)
NB: In reality, I'm not testing one cell at a time. I'm taking a whole lot of cells, mushing them up, and then measuring the glow the mush gives off.
However, there are a few reasons a cell might not glow, and only one of those reasons is the shRNA. Another reason is this: the cells don't glow on their own. They have to take in a gene that makes them glow. It's possible that they didn't get the gene, and so they don't glow. This is called transfection efficiency: the percentage of cells that take up the gene we want them to. Your average collection of cells will have maybe an 80% transfection efficiency. In order to account for this, there is another glowy gene added, the sea pansy one. The sea pansy gene should make the cell glow with or without shRNA. We can tell the difference between sea pansy glow and firefly glow. Or our luminometers can. So the amount of sea pansy glow that the cell mush gives off is telling us how well the cells took up the genes. Now this is where it gets complicated, so pay attention.
For each cell mush, like I said, I get two readings; the firefly glow and the sea pansy glow. What is important isn't the firefly glow number, it's the ratio of the firefly glow to the sea pansy glow.
So, rather than E/C, what we really have is:
f = firefly, s = sea pansy
[E(f)/E(s)]/[C(f)/C(s)] = percent of glowiness in shRNA cell mush compared to regular cell mush
But wait. The shRNA might affect the firefly gene, but it might also just affect everything, and that's why there's less glow. So, and this gets into trickier biology, we also set up an experiment where the shRNA is aimed at something other than the firefly gene, and check the glow again. This gives the non-specific effect, or how much of the loss of glow can be attributed to the shRNA messing up the cell in general as opposed to specifically inhibiting glowiness.
So we've got
n = non specific effect
E(n)/C(n) = percent of glow of cells that are losing glow due to the non specific effects of shRNA compared to glow of cells without shRNA.
transfection efficiency is still an issue
so it's really
so, in order to get the true effect the shRNA is having on glowiness, we need to calculate (get your pencils ready) the first experiment minus the second experiment. But remember, confusingly enough, the second experiment will have a higher number than the first, because what we're really looking for here isn't how much is left, but how much is missing. This is where I think my boss has wandered off into the weeds. My understanding is that the background needs to be subtracted from the result, not multiplied or divided, but he has me multiplying it (I think.) How would you do it?
Meanwhile. One might argue that you don't need to make this into percentages. You could just plot the raw data. Instead of E/C, just make a bar for E, and a bar for C, and show them next to each other. This would make the math a lot easier, certainly. The problem is that different C's for different genes are different, even though they shouldn't be. They should all be the same, and the fact that they aren't irritates PeS. But so in order to compare one gene with another, they all need to be standardized, hence all the division.
If you've been keeping track, this means that we have 8 variables. E(n(s)), E(n(f)), E(s), E(f), C(n(s)), C(n(f)), C(s) and C(f). So how would you arrange all of these to get the true percentage of glow that a cell mush with shRNA has versus a cell mush without shRNA, *because of the shRNA*. So, how much glow is left (or how much glow is lost) between the cell mush with shRNA and the cell mush without, and how much of that is attributable to the shRNA acting on the firefly gene, and not changes in transfection efficiency or non specific effects?
Any and all input is welcome. So are requests for clarification if that will result in input. :) Thank you. Current Mood: outnumbered