Sunday, September 26, 2004

When Being Ahead of Schedule is Bad

I would make a comment on my own lack of meaningful posts of late, but I feel it’s self-evident, so I’ll limit it to this one sentence.

This week has been very busy. I finally managed to get time on a Tuesday to run an experiment and use the flow cytometer to analyze the cells (a flow cytometer basically counts cells and checks them for colors, so if one uses a colored indicator dye to characterize a condition the cell may be in it’s possible to figure out how many of the cells in a population respond to a treatment or not). I’ve been working with a dye that stays green when in the cytosol of cells, but appears red when it collects in the mitochondria of cells (it’s called JC-1).

If the mitochondria aren’t functioning well, they will leak the dye back into the cytosol of the cell, and it will become more red. I’ve been trying to do research on a compound that we think causes mitochondrial dysfunction, and have been trying to reduce the dysfunction (and hopefully improve the cell’s health) by treating with another compound that may increase the cell’s store of protective molecules.

Anyway, a flow cytometer is large, expensive piece of equipment. Our lab doesn’t own one, but Michigan State University has a nice one over in the Biochemistry department that we have access to on Tuesdays. Unfortunately, so does everyone else, so people have to sign up for time on the machine. This is where my problem arises.

Since I work with live cells I’m on a tight timeline, and if I get ahead or behind schedule it can really throw a wrench in the operation. Tuesday I got ahead of schedule, by about an hour. Unfortunately I didn’t catch on to that until I had added my toxicant, otherwise I could have just left them in the incubator longer with the protective compound. In the end they ended up sitting for an extra hour, which can really change an outcome when the exposure to the toxicant is only an hour and a half. Basically, my results didn’t look that good when I was over at the flow cytometer. I’ll go back sometime this week to take a closer look at them and play around with the analysis software.

I’ve also been studying hard for my Biochemistry class. I’m almost up to date on the reading. I’ve actually been taking the time to take notes on each paper as I read it, something I’ve not taken the time to do in the past. I’m hoping it will really help with my retention of the material. My first exam of the semester is tomorrow, but it’s actually for my Pharmacology class. I’ll review the notes a bit more, but there isn’t a textbook or much reading for the class, so I’ve not been spending as much time on it as the Biochemistry course.

Wednesday, September 22, 2004

Free After Rebate - The best things in life are free

Free After Rebate - The best things in life are free

Found this little website a few days ago, thought it was worth throwing up here for others to see. The name really says it all... things that are free after rebate. Don't bet on free shipping though. Perhaps it ought to be called "pay me to ship it to you, and I'll give you the money you loaned me with it back in 3 months."

Wednesday, September 15, 2004

McSweeney's Internet Tendency: The Best Jokes Are Dangerous, An Interview with Kurt Vonnegut, Part One

McSweeney's Internet Tendency: The Best Jokes Are Dangerous, An Interview with Kurt Vonnegut, Part One
McSweeney's Internet Tendency: The Best Jokes Are Dangerous, An Interview with Kurt Vonnegut, Part Two
McSweeney's Internet Tendency: The Best Jokes Are Dangerous, An Interview with Kurt Vonnegut, Part Three

My brothers introduced me to Kurt Vonnegut. For some reason I never got to read him in high school, or if it was assigned I simply didn't read it (how I wish that had been the case with The Deerslayer). It's been some time since I read any more of his work. I believe the last writing of his I read was Breakfast of Champions.

Today I came across an interview with him that was done in 2002. It reminded me of all the things I liked about his writing. I just love reading what this guy has to say. Give it a look see if you get the chance. My favorite part was probably:

Q: You're known for your irreverence as a writer. Is there anything you refuse to write about?

Kurt Vonnegut: Never try to write about your father. Have you?

Q: No.

Vonnegut: Well, if you tried your brain would turn to concrete.

Q: You think?

Vonnegut: Oh, yeah. Men can't do it. You learn about life by the accidents you have, over and over again, and your father is always in your head when that stuff happens. Writing, most of the time, for most people, is an accident and your father is there for that, too. You know, I taught writing for a while and whenever somebody would tell me they were going to write about their dad, I would tell them they might as well go write about killing puppies because neither story was going to work. It just doesn't work. Your father won't let it happen. [Laughs]

Tuesday, September 14, 2004

David L. Spector, Ph.D. - Cold Spring Harbor Laboratory

David L. Spector, Ph.D. - Cold Spring Harbor Laboratory

I went to a seminar presentation today on campus put on by this guy, David Spector. I'd never heard of him, but appartently the graduate students in the Microbiology department invited him and he accepted. The title of his seminar was "Visualizing central dogma in living cells" and it was cool (in the geeky gee whiz kind of cool). He's from Cold Spring Harbor, which is probably one of the most important locations in the history of biological research. He's also got publications in some of the most cited journals in biological research (Nature, Science, Cell, Proceedings of the National Academy of Science). Basically he's an academic all-star kind of researcher.

Basically this guy's lab group developed a synthetic gene that will allow for fluorescent markers to bind to it in it's different stages of existence (as DNA, RNA, or a protein). Having such a system allows one to truly visualize the way in which our heredity is expressed. Along the way they've also made some interesting discoveries about the structure of chromosomes.

What was most remarkable about the presentation was the actual photos themselves of the cells, and the movies of how they change over time. I've been learning about biology for a while now, read a lot of textbooks, but today was the first time I actually got to see (well, see a movie of) a cell producing mRNA, exporting it from the nucleus from the cell, and turning it into protein. We didn't actually see individual molecules, but one sees colors and shapes moving about and with enough background understands what is going on. It was really cool.

What I wonder about it all though is if someone looked at the movies and still photos without any background, what conclusions would they make about it. Or if they knew only that they were looking at a cell and nothing else. Would they make novel observations because the more learned of us are biased towards what we've been taught, and would thus ignore things we didn't have an explanation for, or conflicted with what we knew? I suppose it's just one of those things that makes us shrug and say "Perhaps, perhaps not. We simply do not know."

Sunday, September 12, 2004

How I Spent The Weekend

Mostly I painted the front door of the house, with decidedly mixed success. It's 5:30 Sunday and I started it Saturday around 10am. I'm on the details of the door now, trimming off the excess paint on the window in between the lattice. For such a simple paint job this has taken me forever! Just a plain, all blue door, and I'm still working on it. Most of the door looks nice and blue, I thought I was all done today.

So I take out my single-edge scraper and start removing the excess paint that ended up on the windows. Right away there is a problem. It seems the paint didn't make a very tight bond on the lattice (it's plastic). Little pieces would tear off, the old glue around the edge of the window was coming off oddly, with the end result being I had to go back and touch up all the little spots that lost paint in the process of my removal of the glue and excess paint. The end result was two steps forward and one back. Now I'm waiting for paint to dry again.

I got other stuff done this weekend. Ellie talks all the time about the house being a mess, but it really was this week. She took all the pans out of the cupboards on Wednesday to reorganize and we didn't get them reorganized until Saturday. I was mowing the yard at 9pm on Friday night and didn't finish it all (missed a lot of spots, it got too dark for me to tell what I was doing). We probably did 5 loads of laundry, and discovered I'd left one of our floor mats in the washer soaking for a week. Ooops. Not only that, I left it in there with a red shirt, so now the shirt has dark spots while the floor pink is slightly pink/purple.

On the fun front Ellie and I went over to Todd and Sherie's place on Saturday night and grilled. We had a nice dinner and chat. Today Ellie's been gone most of the day, so I've run a few errands and tidied some of the places in the house. Laundry marched on, and I watched 28 days later on DVD. Scary flick. A zombie flick, done a bit more stylistically. I found myself jumpy and apprehensive while watching it, just as one should with a horror flick. I also caught The 6th Day on the Tivo. That was a stinker next to 28 days later. Arnold does some real bad movies, but I guess sometimes one needs to earn a paycheck.

Friday, September 10, 2004



One of my professors has a son living in NYC. He's done some design work and my Prof mentioned it to me. Thought I'd go check out his website. There's some neat work there, mostly Flash animation and things of that nature, cool stuff.

Tuesday, September 07, 2004

NIH Proposes Free Access For Public to Research Data (

NIH Proposes Free Access For Public to Research Data (

I think this is idea of government funded research being released in the public domain is important to all, in particular to all in the sciences. My brother Rob got me a subscription to the journal Nature last Christmas. I definitely get a lot of value out of it. It was ~$80 for a 2-year student subscription. For a non-student, I believe it is over $200 per year for Nature. The cover price for Nature is $10, and it comes almost every week. For a single articles of scientific literature the prices range from $10-$25 (depending on the journal)!

I'm lucky to be at a big university, because I can get online access to most journals, and for those I can't access I can request copies of articles through an interlibrary loan. I can only imagine how difficult it might be at a smaller school with fewer resources. I probably read 4-5 articles a week, and request 1 or 2. I'd pay incredible amounts if I had to purchase each one. I should actualy revise that statement to I wouldn't read nearly as many articles, because I can't afford it.

In the end, I think it just makes sense that research funded by public dollars should be published in publicly accessible journals, even if the vast majority of people would never read them, and fewer still would understand them. Sometimes I don't even understand them at this point!

Friday, September 03, 2004

Logical Fallacy

New Scientist

The above link goes to The New Scientist website, where they are interviewing a man who did a PhD on "truth." I'm guessing to say that he actually did his dissertation the subject, but I'm just nitpicking again.

I really enjoy it because often times I hear people spouting off advice that they've been told themselves by a coworker/parent/authority, without stopping to briefly themselves if it truly makes sense. I think this is the kind of behavior that leads to "group think" and other failures of reasoning. It's particularly critical of scientists and some lobby groups (the British Medical Association in particular), but I think rightfully so. It also points out a lot of other "fallacy" types that people follow, and I must admit to being guilty of some of them. I like to think I'm a little more reasonable than most, but I'm biased I suppose.

It's only about a 10 minute read (or less), but I think it's got ideas in it that are important for all of us to consider!

Wednesday, September 01, 2004

(Cue Alice Cooper Style Music) School's Back for Fall

School started for me this past Monday. It's been a kinetic blur with everything at the lab and in the class. I got acclimated to not having to go to classes regularly, and now I recall how difficult classes can make it to do quality research.

My situation is better than most of the other 1st year Pharmacology/Toxicology graduate students though. I only have two classes, Mechanisms in Pharmacology & Toxicology (PHM 820) and Molecular Biology (BMB 801). So far I've been digging PHM 820, but it's easy because the professor is one of the better lecturers in the department (Norb Kaminiski). BMB 801 on the other hand... I think this one I'm going to look back and cringe. I'm cringing now!

I'm 25, almost 26 at this point. I've been around the graduate school block once. The way BMB 801 started the professor lectured us about being dilligent in our studies and not having too much fun. She put it much more abruptly than that. Though I can't remember the exact words, they were something like "I've got two children in high school, am a nationally competitive swimmer, and I get my work done, so you can too." I understand why she gave such a stern warning, as there are probably a lot of students in the class that just finished their Bachelor's degree and didn't have to work very hard at it. It just really rubbed me the wrong way. I've heard from a few other people that this person has a reputation for being a bit of a femme fatale, but apparently her husband is even worse (as a lecturer). She's not been bad in terms of lecture quality, thus far. It's early yet though.

She did hand out a review article that I enjoyed reading. It was about RNA interference (RNAi), which is a hot tool right now in molecular biology. The basics of it are small stretchs of RNA can cause longer transcripts of RNA to be degraded, preventing them from making proteins (In the cell DNA is first copied into RNA before RNA is "translated" into a protein). The first publication on RNAi came out in 1999, and I'll wager will result in the Nobel prize for the people who described it. Perhaps I'll try to dig up an example paper from somewhere and write on it. A lot of publications are pretty dry though, so I think I'll have to watch for the right one to come along.

Following Arnold's Address...

Ellie and I were watching the Republican National Convention last night and Arnold was on. I know people say his accent has improved in the last 20 years he's been in the States, but egad, sometimes it's awful listening to him. That's not the point I want to make though. Arnold's accent aside (which was obviously very distracting for me), I really enjoyed his speech. One thing really struck me though as I was listening.

A while back I downloaded Barack Obama's address at the Democratic National Convention (iTunes offers all the speechs for free), as I heard it was pretty good. I did enjoy it (Obama's speech), and noted it was quite positive. So was Schwarzenegger's speech. What was really striking was the similarity of message that came out of their mouths. Both talked about immigrants coming to America and finding something special. Sometimes the politics of the US are not as far apart as some would like to think.

I downloaded John McCain's speech, but I haven't given that one any attention yet since I haven't transferred it to the iPod. If it's exciting perhaps I'll write something else on it.