Monthly Archives: July 2008

isolating mitochondria, strange science, turkey sperm

I tried a kit for collecting mitochondria today. It didn’t work, but it failed in an interesting way, it turns out. Not interesting in a scientific way, unfortunately for me, but it ended up being… humorous…

This kit is supposed to take cells in one end and spit their mitochondria out the other. But there were no mitochondria on the other side. I don’t know if anyone else would go looking though the samples for whole cells, so maybe it wasn’t obvious to other people why it wasn’t giving good yields for the cell type we like. But I did go looking, and I found cells that were not lysed. If they don’t lyse, then they don’t give up the mitochondria.

So I went looking for ways to lyse cells in a way that doesn’t lyse the mitochondria.

Arriaga uses digitonin (detergent) and a cell disruption bomb. The Thurston group isolated turkey sperm mitochondria (I’m too tired to really appreciate how awesome that is) using a combination of Dounce homogenization and sonication. That was back in 1993.

I’d like to share a quote from their paper: “Semen was collected from turkeys (Meleagris gallopavo) by abdominal massage (Burrows and Quinn, 1937).” What I want to know is: who are these Burrows and Quinn characters? And how does someone in 1937 get the job of inventing a procedure to acquire turkey semen?

There’s a story there, by god.



big right turn: analysis of mitochondria

I’ve been running capillary electrophoresis for days looking for a particular chemical reaction. I never found it.In the interest of getting something useful before I leave, I’m switching away from the synaptic vesicle (SV), the subject of my work to date. I have a great deal of emotional attachment to the SV. It’s hard to let go.The SV is what I’ve worked for these last 5 years. The mitochondrion is great, but I know little about it.

To change gears at this stage is terrifying. I’ve never made such a huge turn with so little time to get the task done. We’ll see how it goes. I need to prepare mitochondria, label them, and see what’s inside today. It’s been done, I’m sure, but I should also get some standards and more reagent for the stuff we expect to see inside. It’s going to be exciting!

Here’s something amusing: this is what I first saw in my sample. You want to make sense of that? Because I did. It was Thrilling.

There are lots of different kinds of grad school experiences. There are ones where the goal is to make it work. Other grad students know before starting that it will work but they don’t know until after what it means. In my line of work, we’re contending with both.

If you are a prospective grad student looking for a research program, I offer this advice: figure out which one you like before you start. Then make sure the project you are working on is the one you prefer. Only attempt a project that requires both if you are insane.


the next month's topic, stress, personal life, and a strange article about biomimetics

Dear kind reader,

Thank you for being here. This is a strange time in the life of your host, myself, Peter. I am trying to get the last data for my dissertation. I have 21 days, if I include today which is technically tomorrow. So I won’t be sleeping much in the foreseeable future. Rather than track my interests in the scientific literature, I’m going to chronicle for you the life of a Ph.D candidate in its pupal (pupil?) stages. Shortly I will metamorphose, but until then, stay tuned.

Today, I got up at 7:30 AM and went to the dentist. I got back at 3:30PM and felt a desperate need to acquire a glue stick. I wanted to stick into my notebook a printout of a procedure I wanted to run. It’s the repeat of the procedure I spend 40 hours on this long holiday weekend. And I need it to be stuck in my notebook neatly and securely. So I got a glue stick. And Coffee. The Coffee had nothing to do with sticking things in my notebook.

The 10 cups of coffee may have something to do with the violent diarrhea at 5:00, however. That and the stress.

In any case, I got the procedure into my notebook, and then I had to actually run it. I’m still running (AT 12:43 AM!) it thanks to a crappy epoxy bond. I’m also attempting to apply for a second job to pay for my impending trip to Europe. I am going to Europe to see my sweetie who will be in Germany in August. But right now I am tired and a little lonesome.

I’m running on caffeine, leftover pizza, and sheer determination.

We’ll see if I can keep this up for 21 days.


P.S. What do dolphins, humans and bonobos have in common?

Along the leading edge of their lifting surfaces, they form Large vortices behind troughs whereas flow behind the tubercles forms straight streamlines! Check out the article at Eurekalert!

Actually, this doesn’t apply to bonobos at all.

mercury and table salt

I want to briefly talk about mercury. Mercury is a metal found in nature. It is as natural as sea-salt. It’s a wonderful example of why the word “natural” is not the same as “good.”

How toxic is mercury? According to its Material Safety Data Sheet at Fisher Scientific, it has a toxic dose of about 400 mg per kilogram body weight. At that level it causes tumors in 50% of lab rats. Nobody wants tumors, so I don’t recommend coming into contact with mercury at all. But at the same time let’s put that in perspective.

Table salt has a lethal dose of salt (not tumors – death) only about 8 times as high. that’s right, 3000 mg of salt per kg body weight can kill you (~50% chance of living). Should you avoid salt? No, you need salt. Just don’t gag down grams of it.

Mercury? You don’t need mercury for anything. So avoid it, especially if you are considering having children in the next month or two. But at the same time, don’t freak out about it. Compact fluorescent light bulbs contain a few milligrams of mercury. The post to which I linked is ridiculous. For instance, it quotes a air quality standard of 300 nanograms per cubic meter (of air!) and extrapolates that to soil concentration. Absurd.

The big upshot is that exposure to mercury is an increased risk factor, but so is a well made burger.


Chris Jordan makes art from our excesses and suggests personal responsibility (!) is the answer

This is a great talk about excess, but also about personal responsibility. Chris Jordan’s work takes a number (like 10 million paper cups every day) and makes an image out of it. It’s striking. That Americans use 10 million paper cups a day is almost meaningless. That, on average, every American buys a coffee in a paper cup every 10 days hardly seems like a fact worthy of note. But, in fact, that number translates into an image of a square wall of paper cups as tall as the Statue of Liberty generated every day. It is a strange and uncommon realization that our personal, daily, insignificant choices are (in fact) significant to the Grand Scheme of Things.

From the TED talk by Chris Jordan: Picturing excess:

“My work is about the behaviors that we all engage in unconsciously on a colective level. And what I mean by that is the behaviors that we are in denial about and the ones that operate below the surface of our daily awareness. As individuals we all do these things all the time every day. It’s like when you’re mean to you rwife because you are mad at somebody else… or when you drink a little too much at a party just out of anxiety… or when you overeat because your feelings are hurt.

“And when we do these kind of things – when 300 million people do these kind of things, these kind of unconscious behaviors, then it can ad dup to a catastrophic consequencde that nobody wants and nobody intended.

“How do we change as a culture? And how do we each individually take responsibility for the one piece of the solution that we are in charge of? The answer is in our own behavior. My belief is that you don’t have to make yourself bad to look at these issues. I’m not pointing the finger at America in a blaming way. I’m simply saying that this is who we are right now. And if there are things that we see that we don’t like about our culture, then we have a choice.

“The degree of integrity that each of us can bring to the surface, that each of us can bring to this question, the depth of character that we can summon as we show up for the question of “how do we change?” – it’s already defining us as individuals and as a nation. And it will continue to do that on in to the future. And it will profoundly affect the wellbeing and quality of life of billions of people who are going to inherit the results of our decisions.”