I've been fortunate enough to get assigned to another TA position. This time it is in Dr. Coombs' "Fundamentals of Microbiology" lab. There is only one section with all the students from the lecture, and it meets twice a week.
The students are going to be working with cultures of microbes, including BSL 2 organisms in the second half of the semester. BSL 2 organisms are 'potentially pathogenic' organisms; they can cause disease. Bio Saftey Level is a rating from 1 to 4, with things like Anthrax being Level 4, and non-disease causing varieties of E. coli being level 1.
Tuesday, January 30, 2007
Saturday, January 20, 2007
Cleaning for Mg:Ca Analysis: Problems and Solutions
I collected around 40 individual G. bulloides for the first 15 or so depth intervals from the core. I seperated them into two sets of 20 individuals each and carefully crushed the test chambers open in prepartion for cleaning them for Mg:Ca analysis. This gave me 30 samples, which were put into certified metal free tubes on a rack. Even though they were certified metal free, I still treated them to a long heated acid bath to ensure that there were no metals that had collected in them, such as with dust. I then went to Dr. Farmer's lab at Hofstra for the cleaning at around 9 in the morning. The rest of the cleaning work was done inside of a negative pressure hood, to prevent metal bearing dusts from contaminating them. They were then put through a series of treatments, the goal of which was to remove all clay minerals and wash away any Mg or Ca crusts (non-biological) that had accumulated after deposition on the ocean floor. A small amount of methanol (for clays) or acids (for leaching) would be added to the tube and then siphoned off. I also treated the samples to a boiling bath of strong Hydrogen Peroxide, to destroy any organic materials that may also have accumulated, using a sonicator at many steps to aggitate the material. Leaching in a weak acid was the penultimate step before final dissoution. It was after leaching, and this was around 6 or 7 at night, that I realized that the tiny amounts of material were missing, they had either been dissolved at one of the acid steps or sucked up by the vaccuum. That was unfortunate.
So several days later I collected a small sampling of forams, not necessarily all G. bulloides, but similarly shaped and with similarly thin test walls, from a 'practice' jar of washed material. There were four tubes, with around 20 crushed individuals in them each. I then used the same procedure as I had previosuly used to clean them, and after the weak acid leach, they were still there and looked good.
So its possible that I had previously sucked them up with the vaccum, or that I had crushed them too finely, which allowed them to dissolve in the various acids. But it looks unlikely that carefully crushed tests will be dissolved by this procedure, which of course is to be expected, since many other workers have used it with success, including Dr. Farmer.
Now I will have to finish picking the foram samples and clean them, hopefully there won't be any problems with this round.
So several days later I collected a small sampling of forams, not necessarily all G. bulloides, but similarly shaped and with similarly thin test walls, from a 'practice' jar of washed material. There were four tubes, with around 20 crushed individuals in them each. I then used the same procedure as I had previosuly used to clean them, and after the weak acid leach, they were still there and looked good.
So its possible that I had previously sucked them up with the vaccum, or that I had crushed them too finely, which allowed them to dissolve in the various acids. But it looks unlikely that carefully crushed tests will be dissolved by this procedure, which of course is to be expected, since many other workers have used it with success, including Dr. Farmer.
Now I will have to finish picking the foram samples and clean them, hopefully there won't be any problems with this round.
Tuesday, January 09, 2007
Wintersession
For the intersession during the winter break, I had to.
- I need to contact Dr. Farmer over at Hofstra. (done)
- Prepare a new outline for a Thesis Proposal (done)
- Contact Dr. Forster at SUNY Stonybrook about her program (done)
- Complete SUNY Stonybrook PhD application.
- Prepare a draft cover-letter for new job applications.
- Pick 40 G. bulloides to later be analysed for Mg/Ca ratios from all of the 1H1W and 1H2W intervals.
I am waiting on any kind of response from Dr. Forster. I have to wonder at how they react to emails from people that they don't know, asking to work with them and asking about grant money. Seems like it would normally sound suspicious. Maybe I can pretend next time to be a Nigerian Bank Manager. I suppose that they expect it to be part of the territory that comes with being a professor in a programme.
Outlining the a new proposal for my thesis went quicker than expected. Prof. Christensen had previously said that I should use her other student's theses and proposals as a way to structure it. But I hadn't done that. I tried it this time, and it sure was a lot more helpful. The difficult part was deciding what sections to put everything into, but seeing that other students had just flat out broken it up into the study area, background on the techniques and science, and then an explanation of their method, was just a sensible way of laying it out. This should make the writing of it go quickly.
As far as cover letters and essays for applications, I have to get going on that.
Picking the samples has been a mixed experience. I focused on my previous picks from Jim's material, pulling out what I now recognize as G. bulloides. I've gotten through all of 1085B 1H1W, and now just have 1H2W to go through. After that though, I am going to need to either sieve some more material to get up to 40 G. bulloides for each point I want to sample down the core, or go through the rest of Jim's and see if there are any to get from there. I'll probably end up doing both.
Wednesday, January 03, 2007
More forams
Met with my Professor today to go over what I need to get done before the semester starts. We're going to meet for another couple of days to review what I've gotten done. I need to reorganize my Thesis Proposal, so I can present it to a committee for approval. I also need to actually select who will be on my Thesis Committee too. Apparently I might be able to include Dr. Farmer on this, even though she is at Hofstra (and in a different department on top of that). That should be helpful, since she has direct experience with this kind of work. I will need to contact her soon to set up when to come to the lab and find out exactly how many specimens to pick for each level.
Thats the big task right now, picking the specimens. I started by trying to pick out G. bulloides from Jim's slides, I got through half of one section of the core and was barely able to find one. I think I might've picked too liberally when I was looking for Nq. pachyderma previously, and taken up all his G. bulloides. So I went back to my old slides and really started hitting a roadblock on just what defines which organism. I definitely picked a lot that weren't Nq. pachyderma, in the early slides at least. I was able to get some G. bulloides out of them too. But now I am not at all confident in my understanding of which characteristics define which. Yes, I have Kennet & Srinivasan right in front of me, but the descriptions just seem like they can go either way on so many individuals. I ended up spending a long time in the lab, but got nothing done with it.
Before all that I had to clear up an issue with financial aid. They had cut a refund check for me early in the semester, but when the TAing tuition waiving came through, they shut off the financial aid. That meant that the check that the school had cut for the refund wasn't being covered by my Financial Aide, so now I owed them for it. Luckily, all that needed to be done was to have a stop put on the check.
After that, I gave the biology office my probable schedule for Spring. Hopefully, I will be able to get another TA position. The professor in charge of doling out the positions had only picked up the student schedules earlier this morning, so they shouldn't've assigned anything to anyone yet. On top of that, one student that was a TA last semester isn't doing it again, so that should mean I am pretty certain to get a position.
Thats the big task right now, picking the specimens. I started by trying to pick out G. bulloides from Jim's slides, I got through half of one section of the core and was barely able to find one. I think I might've picked too liberally when I was looking for Nq. pachyderma previously, and taken up all his G. bulloides. So I went back to my old slides and really started hitting a roadblock on just what defines which organism. I definitely picked a lot that weren't Nq. pachyderma, in the early slides at least. I was able to get some G. bulloides out of them too. But now I am not at all confident in my understanding of which characteristics define which. Yes, I have Kennet & Srinivasan right in front of me, but the descriptions just seem like they can go either way on so many individuals. I ended up spending a long time in the lab, but got nothing done with it.
Before all that I had to clear up an issue with financial aid. They had cut a refund check for me early in the semester, but when the TAing tuition waiving came through, they shut off the financial aid. That meant that the check that the school had cut for the refund wasn't being covered by my Financial Aide, so now I owed them for it. Luckily, all that needed to be done was to have a stop put on the check.
After that, I gave the biology office my probable schedule for Spring. Hopefully, I will be able to get another TA position. The professor in charge of doling out the positions had only picked up the student schedules earlier this morning, so they shouldn't've assigned anything to anyone yet. On top of that, one student that was a TA last semester isn't doing it again, so that should mean I am pretty certain to get a position.
Tuesday, January 02, 2007
The Road by Cormac McCarthy
Got this book for Christmas, which is funny because I had picked it up in a bookstore and thought it looked interested but ended up not buying it. So I lucked out and ended up having it anyway. Just finished reading it, really interesting book. Its about a father and son, neither of which are named at anypoint in the book, wandering through the world after what seems to have been global thermonuclear war. The world is completely destroyed. The inside flap of the dust jacket says that they are walking through "burnt America", which says it all. Everything everywhere is completely burned out. There event happened in the man's lifetime, when his wife was pregnant, and the books starts years later with just him and the kid. The descriptions in the book push the sensations of the charred out world where the only thing that seems to move is a permanent cover of ashes. There's no sun anymore, or at least you can assume it still exists beyond the never ending overcast of the sky. Only a diffuse light exists during the day. McCarthy describes mornings as 'palings', and night is absolute blind blackness. The only things that are alive in the book are humans for the most part. We once hear a dog parking, but that stops before long. Hell, people are capturing and eating other humans, so of course they've done away with dogs, cats, etc. Pets, I suppose, are pretty superfluous in the apocalypse. The only other time any animals are mentioned is during a nightmare of two with hideous monstrous animals, and then one scene where there are snake. A group of men pull open a peice of hill to get at a mass of hibernating snakes within it and just set them on fire. McCarthy describes it as little more than them wanting to destroy something that represents evil.
I don't think it necessary to view the book as a science fiction novel. It doesn't make sense that way. Nuclear war would be destructive, but here, its like every square inch of the planet was hit with a flame thrower. And every animal is dead, there's never any insects, birds, worms, nothing. But humans are still alive. The coasts at some points are completely littered with millions of tiny fishbones, and the oceans are just churning gray masses. The description of rivers are great, they're just these dead, whirling black slicks with greasy froth and scum all over them. The only food that they come across are tinned goods, and it seems to be what everyone survives on, either that or other people. The man and the boy are like concentration camp victims, but they seemed to have walked from Virginia, or even further north, to the southern tip of Florida. So no its not a science fiction book. Its almost more poem than prose. McCarthy also doesn't use much punctuation, which can be annoying, especially with dialog. Its easy to forget who's talking or thinking any particular line, or if its even being narrated when you start reading the sentence, which, I suppose, must be the point.
Its almost funny to even think of it as a "post apocalypse" story. Just compare it to the TV show Jerhico or Mad Max or anything from the 'after the end of the world' genre and you can see that its just completely different. There are hints of the post-annihilation history, but its muddled and infrequent. "Blood Cults" and "bull drums" are completely used as props to reinforce the mood of the book. Its like when a horror movie never gives you a good look at the monster. You know its hideous, and therefore it is, you don't need an accurate and detailed description, its as horrendous as anything you know, because you've more or less made it up.
Its the descriptions that I think come out most stronly in the book. Even though the whole world is nothing by gray dust, black ash, and scorched soot, where even the snow is gray, you still manage to get a 'vivid' impression of it. You can feel how freezing cold it is, with minimal sunlight during the day, and nothing but scavenge wood or gas to burn for a fire.
The story ends oddly, but I guess that McCarthy figured he couldn't have an unhappy ending. You definitely feel completely hopeless for these two completely pitiful people through most of the book. Half the time you just hope that the man snuffs out the kid before some one roasts him over a spit or wears his skin for a hat. If the narrator said "but in reality, this wasn't earth, the man and boy had died in the attack and now they were wandering through hell while everyone else was alive', you'd beleive it. They're traveling down the road, because its the only thing around. Its all asphalt and oil, and the novel appropriately ends with someone telling the boy to get out of the middle of the road. The other thing that I noticed about the novel is the physical book itself. At first I thought it was just poorly cut, but after a little while I realized that the pages must've been made uneven on purpose, gives you a feel for it being something to be left during the apocalypse.
Here's a page about the author, from the looks of his other titles, he doesn't seem like the most jovial guy around:
CormacMcCarthy.com
From his page I see he apparently is the author of "All the Pretty Horses", which was made into a movie. Never saw it.
Random House has a pretty nice looking page for the book, but from the looks of the url it will change with his publication history, so it might not allways be for "The Road".
I don't think it necessary to view the book as a science fiction novel. It doesn't make sense that way. Nuclear war would be destructive, but here, its like every square inch of the planet was hit with a flame thrower. And every animal is dead, there's never any insects, birds, worms, nothing. But humans are still alive. The coasts at some points are completely littered with millions of tiny fishbones, and the oceans are just churning gray masses. The description of rivers are great, they're just these dead, whirling black slicks with greasy froth and scum all over them. The only food that they come across are tinned goods, and it seems to be what everyone survives on, either that or other people. The man and the boy are like concentration camp victims, but they seemed to have walked from Virginia, or even further north, to the southern tip of Florida. So no its not a science fiction book. Its almost more poem than prose. McCarthy also doesn't use much punctuation, which can be annoying, especially with dialog. Its easy to forget who's talking or thinking any particular line, or if its even being narrated when you start reading the sentence, which, I suppose, must be the point.
Its almost funny to even think of it as a "post apocalypse" story. Just compare it to the TV show Jerhico or Mad Max or anything from the 'after the end of the world' genre and you can see that its just completely different. There are hints of the post-annihilation history, but its muddled and infrequent. "Blood Cults" and "bull drums" are completely used as props to reinforce the mood of the book. Its like when a horror movie never gives you a good look at the monster. You know its hideous, and therefore it is, you don't need an accurate and detailed description, its as horrendous as anything you know, because you've more or less made it up.
Its the descriptions that I think come out most stronly in the book. Even though the whole world is nothing by gray dust, black ash, and scorched soot, where even the snow is gray, you still manage to get a 'vivid' impression of it. You can feel how freezing cold it is, with minimal sunlight during the day, and nothing but scavenge wood or gas to burn for a fire.
The story ends oddly, but I guess that McCarthy figured he couldn't have an unhappy ending. You definitely feel completely hopeless for these two completely pitiful people through most of the book. Half the time you just hope that the man snuffs out the kid before some one roasts him over a spit or wears his skin for a hat. If the narrator said "but in reality, this wasn't earth, the man and boy had died in the attack and now they were wandering through hell while everyone else was alive', you'd beleive it. They're traveling down the road, because its the only thing around. Its all asphalt and oil, and the novel appropriately ends with someone telling the boy to get out of the middle of the road. The other thing that I noticed about the novel is the physical book itself. At first I thought it was just poorly cut, but after a little while I realized that the pages must've been made uneven on purpose, gives you a feel for it being something to be left during the apocalypse.
Here's a page about the author, from the looks of his other titles, he doesn't seem like the most jovial guy around:
CormacMcCarthy.com
From his page I see he apparently is the author of "All the Pretty Horses", which was made into a movie. Never saw it.
Random House has a pretty nice looking page for the book, but from the looks of the url it will change with his publication history, so it might not allways be for "The Road".