Tuesday, November 30, 2004

Our cat has discovered a new hiding place now that the Christmas tree is up... Posted by Hello

Monday, November 29, 2004

Experimental Disasters

A discussion with my brother Rob this weekend inspired a post from me. Naturally we were talking shop about what's going on in our respective labs (his at Texas A&M, mine at Michigan State) and somehow we got on the subject of experiments getting screwed up.

It's a semi-regular occurence in research that someone forgets a step, or does it incompletely, or incorrectly. Little errors can have huge implications when it comes to the results. I thought I'd share some of the more spectacular ones I've heard of.

The first story I was first told when I was an undergraduate at Michigan State in a biochemistry class.
There are a lot of ways to examine DNA, but one is to run it through a porous gel so that it separates into bands of different weights. DNA is invisible though, so to visualize it one can use a dye called Ethidium Bromide to stain the DNA (it wedges itself in the spaces between bases on a strand of DNA). Ethidium Bromide glows brightly under UV light, so one can shine a light UV light on Ethidium Bromide stained DNA and visualize the band and determine the weight (and then approximate the size of the strand from that).

The problem with Ethidium Bromide is that it is a carcinogen, owing to the fact that it wedges itself in between DNA bases (this can cause mutations when the DNA is copied prior to mitosis). My biochemistry teacher was explaining this to us, and to emphasize the point told us of a new undergraduate he had hired in his lab. The student had stained a DNA gel and done his experiment, then walked off to the restroom after he finished. He did not remember (or didn't realize it was important) to remove his gloves and proceeded to put contaminate everything he touched with Ethidium Bromide (fortunately it can be cleaned off without a great deal of trouble). The professor told how they had to walk around the room with a UV light, following the Ethidium Bromide trail to the bathroom. The student didn't work for them after that, and I never heard at which point he remembered to take of his gloves.

Such stories are not uncommon to hear from chemical safety officers at universities, particularly when it comes to radioactive isotopes. Radioactive isotopes are useful in research because we can easily detect them, so attaching them to something that is normally undetectable can make such things easily detectable. The problem is they stick around for a long time. If one spills a radioactive material one may have to close off the area for use. An example that always sticks in my mind is the story about a person who had spilled a radioactive solution on the floor in the lab and accidently walked in it, getting the isotope on their shoes. The Office of Radiation, Chemical, and Biologicial Safety (ORCBS for short here at MSU) cleaned up the mess, and took the person's shoes! Apparently they were a good pair of shoes too, since the person had to call back every few months to see if their shoes had "cooled off" enough to be safe to wear. That's one case were a spill in the lab can put a real cramp on your style.

The next story was relayed to me when I was working in the Food Science and Human Nutrition department at Michigan State. bemoaning an error I made in mixing some buffers, using up most of a reagent that was about $100 per milliliter. The student I talked with said not to worry, she'd seen far worse mistakes. She told me the story of another student who had been working for a professor that did feeding studies (it was, after all, the nutrition department) in rats try to design better diets for people. For feeding studies one usually has to feed rats for a few months and track their weight gain. At the end of the study one does normal clinical chemistry on the blood of the animals to understand better how effective the diet was. Such a study gets to be very expensive because it costs money to buy, house, and feed rats (as well as graduate students).

At the end of the experiment the red blood cells need to be separated from the rest of the blood, so one uses a centrifuge to spin the blood and get the red blood cells at the bottom of the tube and the remainder of the blood (called plasma or serum depending on how it was treated) for clinical chemistry checks. When using a centrifuge it is important to make sure the weights on either side of of the spinning rotor are similar, otherwise the imbalance can damage the machine (consider an unbalanced washing machine on the high spin cycle can rock back and forth quite a but; now spin it 10,000 times faster). If things got really bad a centrifuge can fail in a spectacular manner.

The professor told the student to be sure to balance the rotor, and use water to even the weights of the blood samples. The student followed the instructions, adding water to each blood sample so that they were all the same weight, in the process ruining the blood samples (adding water to the blood will can the red blood cells to burst because there isn't enough electrolytes like sodium in the water). A case of months of work being partially undone in half an hour. Doh!

The final story I got was from Rob, who told me this story was told to him when he got to Texas A&M. I think it's the most impressive of the three.

Occasionally in research there are reagents left over. Being collegial, investigators often offer the leftovers to other investigators in case they have any use for them before sending the stuff for disposal. Apparently a researcher had finished with a tank of chlorine gas (a highly reactive, corrosive, poisonous, and useful reagent). It had been quite some time (years) since it had been used, so it was given to another group. The safety cover for the top of the gas cylinder had become rusted, so before a new regulator could be placed on the tank the old safety cap and regulator needed to be removed. A pair of graduate students were assigned the task of putting a new regulator on the tank so that it might be used. Despite their best efforts the safety cap couldn't be removed, so one took out a hammer and gently tapped on the cap to remove it. Success! Now the old regulator needed to be replaced. The succesful student stepped out of the room for a while to take care of something, leaving the other student to remove the regulator.

This is when things get stupid. The remaining student decided to try the hammer approach on the regulator. As Rob told me the story he described this stage like so:
A person in another room said all they heard was a "tink, tink, tink.... tink... Tink... TINK... OH SHIT! HISSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS"

The student knocked the entire top off the tank, producing a glorious stream of chlorine gas. Being that chlorine is a highly reactive, corrosive, poisonous, and useful reagent the student high tailed it out of the room and slammed the door behind him. Fortunately no one was injured in the faisco, other then the pipes in the ceiling of the room which the chlorine corroded quite badly. What's the moral? I'd like to phrase it like a professor put it to me when talking about how to plan an experiment: You've got to look at the tools you've got available to you and decide how to best approach a problem. If you need to cut a piece of 2x4 you can manage to do it with a hammer, albeit slowly and messily, or you could use a saw. That's where wisdom and experience come into play. So the moral is: a hammer is not the tool of choice for sawing wood or fixing the regulator on a tank of compressed gas.

Sunday, November 28, 2004

Here's one of the few photos that I thought came out nicely from the baby shower yesterday. Ellie and I have been quite frustrated lately with our Kodak DX4900 digital camera and its ability to autofocus. Unless one is very careful the photos end up blurred, I think because the delay between the button press and the photo is more that one normally expects. How I wish we had known a little more about digital cameras before we spent the 2001 tax return on it (it was our patriotic duty after all to spend the money the government returned to us).  Posted by Hello

I wanted to take some photos Thanksgiving morning after the snowfall we got Wednesday night Posted by Hello

These were all taken in our backyard Posted by Hello

A closeup for the final photo Posted by Hello

Friday, November 26, 2004

Things That Remind Me How Bad & How Good We Can Be

Being the Friday after Thanksgiving and something of a vacaction, I took advantage and spent some time this morning to watch an episode of NOVA that I had waiting for my on the Tivo. It was about the Great Escape, a story about Allied airmen imprisoned at Stalag-Luft III during World War II escaping from the prison camp. A fascinating story to be certain, but there are many of those from WWII. What got me choked up was some of the comments of the soldiers there.

Toward the end of the episode some of the men who had stayed behind in the camp (76 escaped in one night via tunnel) they talk about how the Great Escape greatly annoyed Hitler, so much that he ordered that all the escapees be executed (in violation of Geneva Convention rules). His advisors talked him down to 50. Compared to what the Jews , Gypsies, and homosexuals suffered this isn't much, but there is a reminder that really stuck me about how cruel we can be to each other.

Some of the prisoners, now old men, talk about there being rules to these things, and when people are lined up and shot it isn't fair. I'll agree with that, but there is so much that isn't fair about war this didn't strike me. What struck me was when one of the men who had been left behind was talking about one of the executed airmen, one of his bunkmates. He said he felt sad because the man who died never got to see his child, and his child never got to meet him. His comment is what really hit home for me. My heart is wrenched when I think about how it would be if I died before Alexandra arrived, how much we would both miss in our lives. It brings tears to my eyes when I think about it.

I thought about what horrible things we people do to each other when we make enemies of each other. Its so deeply saddening when we think about people as those who just want to be happy. They have mothers, fathers, brother, sisters, wives, children. They care about where their next meal is coming from. They want to be able to enjoy a sunny day, or have a walk and enjoy the company of friends. Then to hear about human life being so disregarded in concentration camps, or summarily executed for what people believed was their duty. These things about humankind so frustrate and trouble me.

Then there are things that are uplifting. I was thankful that one occured alomst within the same minute of the talk about the escapees being executed. The Luftwaffe captain that ran the camp was so horrified when he heard what happened that he allowed his prisoners to build a memorial outside the prison camp to the men who died. The idea that even in war that we can realize the suffering and humanity of those we fight and respect them is what makes me think that sometimes we can overcome the things that seperate us most and recognize the things we have in common.

There are probably millions of stories like that, I just wish I heard more of them.

Monday, November 22, 2004

Arguing with Myself

It was a few weeks back that I was reading Nature and an article got me thinking about human embryonic stem cells. Some researchers in Chicago managed to derive stem cells from a 4-day old embryo, a first in the field. Previously the earliest one could manage this was around the 6-day mark. The natural question is “What is the significance?”

What I think is significant about it is that is a step closer to being able to derive human embryonic stem cells without destroying the growing embryo. Ethically and scientifically I think it would be a great achievement to be able to derive embryonic without destruction of the embryo. Most interesting in my mind though is would it become nationally acceptable to use government money for human embryonic stem cells if the destruction of the embryo was not necessary. It would seem to me that it is the destruction of the embryo that is the most troubling aspect to people who oppose human embryonic stem cell research. If one could get embryonic cells early enough that normal development could occur (identical twins are the product of a single embryo after all), what is the harm?

In the end though, what is done with the embryo even if it can survive? If it is not implanted it will never mature to being a fetus (barring some significant advances a la Brave New World). If it becomes ethically acceptable because the embryo is not destroyed, but the embryo/fetus/baby will never be born without serious interventions then what were we debating about all along? This troubles me deeply.

When I tried to talk to Ellie about it she got rather upset, as she’s very much opposed to human embryonic stem cell research. I hadn’t expected her reaction; I thought that if the embryo wasn’t destroyed she wouldn’t find it an unacceptable idea. Instead I got an earful, but also a valuable insight. She told me she felt that the cells belonged to the embryo, an idea that I hadn’t considered. The idea that the genetic material should belong to that embryo was new to me, but now I see it as important.

I think it raises a different prospect if we take the ethical high road and say the embryonic tissue belongs to that individual from which it was derived. If fertilization occurs in vitro, I’m of the opinion that it would be acceptable to bank embryonic cells much like we bank cord blood today (which we briefly considered for Alexandra before we saw the astronomical cost), as long as it didn’t damage the embryo and the use of the stem cells derived was left entirely to the individual from which they came.

Of course all my ethical pondering at this point is moot. Scientists still can’t derive human embryonic stem cells without destroying the embryo, so it’s all science fiction I suppose.

Saturday, November 20, 2004

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Thursday, November 18, 2004

Pressure Release

Exams for my classes are done for now. I won't have another one until exam week, so there's plenty of time to forget everything I tried very hard to learn. I was telling Ellie about last night's Pharmacology exam, and I realized I might be making my performance out to be worse than what it really is.

When I was an undergraduate all we got were multiple choice tests. I think that comes with the territory at a big university, or the Scantron company has made a deal with the devil and Michigan State. I'm thinking the former. When taking those tests often one of the answers jogs your memory and you know it's correct. One can walk away with a pretty good idea of how they did.

I haven't had a multiple choice test now in at least 3 years. Questions may sometimes be open to interpretation, and most try to get you to make some leap in understanding rather than remembering A influences B, though that has to be known too. The point is that grading is not as objective as it is subjective, though for the most part professors are very fair about the questions they ask. The area that troubles me is there is so much information to digest that one cannot reasonably study it all well enough to give a "perfect" answer. An excellent example came once again from my Biochemistry test.

We had a lecture on retroviruses, and spent a lot of time focusing on the life cycle of HIV-1 and how it replicates itself into the genome. I must have spent 1-2 hours learning the replication mechanism for HIV, which was a large part of the lecture. On the exam there wasn't any question on viral reverse transcription (the process that HIV goes through to become part of the host's DNA), instead there was a question on how a small part of the virus can promote a different region of expression. This was a tiny part of the notes compared to descriptions of the life cycle and mechanism of reverse transcription, and that was what was on the exam. I didn't have a good answer.

So when I talk to people about how I do on an exam I'm usually thinking about the part that I didn't know, not the parts that I did know. I've also got a superstition that if you think you did well on an exam you did not do as well as you thought you did, and if you think you did poorly you probably performed better than you think. That's why I don't like to talk about how an exam went. I usually just say "It was tough, but the questions were fair. I guess we'll see."

Tuesday, November 16, 2004

A Change is Upon Us

I've gone commercial. I noticed when I was logging into Blogger the other day there was a short note on the first page after sign-in that said Blogger/Google "was still taking applications for AdSense" (those weren't the exact words). AdSense is Google's advertising arm, delivering ads based on content that's on the page.

Since there was previously ads on the page I figured hey, why not get paid to serve ads. Even if it's not much, as long as it's not very involved then it's not a problem for me. Once I signed up I discovered there was also an option to have Google searches run from my site, and if I got clicks for advertisers on the search results then I get a few cents. Interesting. I like the idea of being able to hit a Google search from my blog, so I added that too.

At this point I still haven't figured out how to get the darn ads over to the far right like I want. They look really annoying right now. The search bar isn't bad though. I've try playing around a I think, but not any more tonight. I've got a Biochemistry exam at 7pm.

I've been studying for it for at least two weeks, and at this point I think I'm as prepared as I could reasonably be. The real question will be how will I perform on the Pharmacology exam I have tommorow, which I haven't invested as much time in studying for. I've worked on it some, and I'll do a bit more tommorow. For know I think it's time to go test my knowledge.

Thursday, November 11, 2004

Time Waits for No One

Another week marches on. Things have been speeding by at work and
home. Every week I feel like a work quite a bit at what's going on in
the lab but don't come up with that many data points. I've finally
finished the analysis of the experiment I started on October 13th (a
time course of response to specific inhibitor an adapter protein). Now
we're planning an experiment to test different doses of the inhibitor.
I'm pleased with how things have been going, but of course I would
always like to see more progress.

Alexa's growing bigger by the day. She moves around quite a bit, and
of late has given us a bit of a scare. Ellie and I went to the OB a
few days back and she looks healthy, estimated at 4lbs. What was a bit
of a concern was the level of amniotic fluid was less than expected, a
level described as "borderline." Ellie's been quite concerned, but I
keep trying to tell her it's one snapshot in time, so jumping to
conclusions about what's going on is premature. That doesn't stop the
worry though. We'll be going in more often to keep an eye on her
(Alexandra's) progression. Ellie received some meds to encourage
Alexandra's lungs to mature more quickly in case she were to come
early. Apparently when the amniotic fluid gets low there is an
increased chance of labor coming on quickly, so as a contingency the
meds were given. We'll have to keep an eye on things and with time
we'll know better what to expect.

At home I've got a few new toys home that came with my birthday
passing (26th one). I put together several Best Buy gift certificates
I received to buy a new 16x DVD burner. Funny thing was I looked for a
good name brand at a good price and ended up buying a Plextor PX-716A,
a very new burner. After I got it home I was reading about it and came
across some grumbling about the quality of the burns it makes. I've
been running the diagnostics on some test burns I've made on some
DVD+RW discs I bought and thus far the results have been ok in terms
of quality. Not perfect, so I'll do a bit more testing before I decide
whether this guy is heading back to Best Buy to trade for a different

Tuesday, November 02, 2004

I'm an Election '04 Grump

oon it will all be over. The bickering, name calling, forgery, and misstatement of fact will be pointless come close of the polls tommorow. Good ridden. Both major party canidates have earned my contempt, and their parties as a whole as well. I'll be happy to cast my ballot and have it all over with.

It was a slow Halloween at our house.  We only got ~30 people stopping by for candy, which we found rather suprising. I chatted briefly with Dr Kaminski this morning, and he observed the same thing. Perhaps it was too cold for some folk out there. Whatever the case, we had quite a bit of candy left over.

I watched Jeepers Creepers last night while Ellie stayed in the main room, as she wasn't interested in seeing anything scary. I give a "Meh, nothing notable" review. I thought it was at its scariest at the beginning rather than the end.

Of late things have been running along relatively smoothly in the lab. I always think things will got faster than they really do. Guess I'll learn to gauge it all better with experience. I'm finally getting to the stage where I can analyze some gene expression data from the time course treatment I gave the cells a few weeks back. Since I was starting from scratch it does take a bit longer to make sure everything is running like it's supposed to, and there are steps that are new to me too. I hope to have data by the end of the week that will tell me whether the experiment was a success. I already know that the protein whose expression I was trying to knockdown didn't fall much over the time points I looked at, but we won't really know what the next step to take will be until we also know how the gene that encodes the protein changed as well. If it went down a lot and the protein went down a little, then it will be back to the drawing board or time to drop the project and try something else.

If the gene went down a little and the protein went down a little, then we may just have to redesign the component we used to inhibit the gene expression. I'm hoping that will be the case, as I think it would be pretty darn cool to see how the protein we're looking at affects the mechanism of the toxin (stuff called dioxin) we're studying.