Category Archives: Humor

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.

-Peter

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.

-Peter

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.

-Peter

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.

Getting enough sleep is key, but how much is enough?

I posted about some gumption traps before, and I mentioned caffeine as one of my favorite solutions. The underlying issue, of course, is sleep. Not too long ago, I made a note of the fact that even the simplest creatures imaginable have something like sleep. Evidently, it is pretty important.

According to this article over at news.yahoo.com, most people perform best on about 7.5 hours per night. My experience is consistent with the results presented in the news bit. Too little sleep leaves me uncreative and groggy; too much and I am lethargic. There is a balance to be struck. My problem is mornings. I hate getting up. I always feel less tired when I go to sleep than I do when I wake. That makes no sense. It drives me crazy. I’ll be rearing to go at midnight, and I force myself to go to bed then have to meditate to calm down enough to fall asleep. Then I wake up 8 hours later when the alarm goes off and I fell like my world will cave in if I don’t get 4 more hours of sleep. It’s absurd.

I’ve tried polyphasic sleep (I live a 7 min walk away from my work, so I can go home to sleep if I want). I’ve tried the rolling 28 hour day. They both left me with horrific nightmares. I felt like I was on a fast track to a mental breakdown. It was not good. So I muddle along.

I have mentioned nootropics here as well. I have not tried anything except caffeine. Maybe that’s why people get into them. Matt (that other guy on this site) sent me the sleep article; he also tells me that the use of nootropics is common among pharmaceutical representatives (he used to be one). Go figure. Think of science as the Sport of the Mind, except that there’s no rule against doping. Makes me want to go get a bottle of Nerve Tonic.

-Peter

a bad day for mice makes the future a little brighter for humans

I read an article in Nature news about about a cure for palsied mice. It brought to mind a little quote a while back that made me chuckle. A researcher was asked how she felt about how close science was to a cancer cure. She replied “If you’re a mouse with cancer… I have good news.”

 

Joking aside, it is a lot harder to do medical research on humans. I read the original paper that inspired the news bit and I was struck by this graph. There are 3 lines: mutant palsied mice, identical mice injected with a placebo and identical mice injected with human brain cells. The mutant mice lack a functional kind of cell that surrounds and protects the other brain cells. These glial progenitor cells become cells that produce myelin. Brains without proper myelin produce symptoms like Multiple Sclerosis. If a mouse accepts the new, human cells, the mouse recovers. So why not just skip the mice and cure people? I imagine there are a hundred good reasons, but take this graph as one example.

The fact is that that if you are a mouse with Multiple Sclerosis, I don’t have very good news. The red line is your best bet, and even there you don’t have a great chance of ending up ‘cured.’ This will take a bit of work before it’s time to try this out on people.

But it’s a good step, and that’s what it’s all about. I am really impressed with this kind of work. Look at the scale of the X axis on that graph: that’s a year of someone’s life devoted to taking care of a population of sick mice. I think this understated fact is the really amazing thing about science. It is not about a smart loner spending a few weeks in a laboratory and then fighting the ‘establishment’ for recognition. It’s about year-long endeavors that, in the end, produce one graph. That graph represents a small, hard-won step toward a loftier goal. I find it more noble to work so hard for a small, steady step than to blaze brilliantly onto the scene with claims of a scientific revolution.  The fact is that most ‘scientific revolutions’ aren’t.

-Peter