31 May 2004

Holiday, apparently

South Texas has begun its regular "heat that beats you like clubs when you walk outside" only slightly later than scheduled. I was greatful for the repreive, I suppose, with a cooler spring this year than last.

Today is apparently an American holiday that, being Canadian, holds no special importance for me. I was in my office trying to work bu tnot getting very far, as my main unfinished job right now is to order supplies for my students. And that means I need to get quotes for shipping costs, that sort of thing.

My major task for next month is to somehow start getting grants and manuscripts happening. I'll keep you posted.

27 May 2004

Not yet, maybe soon

I still haven't managed to get anything new started, but I think I'm getting closer. The search committee stuff, and the two on-site interviews next week, are both taking major chunks out of my time. Luckily, one way or another, those searches should be over in two weeks.

26 May 2004

Road trips

I got back yesterday from a pleasant and productive trip to the Austin area. I visited with my colleague Virginia Scofield, but more importantly, got to visit several people in the University of Texas Austin Section of Neurobiology. Although the visit was put together on rather short notice, I was able to meet a few people, and quite a few people attended a talk I gave. I was pleased that they were asking very perceptive questions, and seemed genuinely interested in the story I had to tell.

The downside to visiting the particular day I did was that UT Austin was engaged in cleaning its entire power system. Apparently, this involved blowing steam through some massive turbines. This process is going on apparently all week, and it involved noise like few things you've ever heard. Have you ever stood next to a jet engine at full throttle? Louder. They had construction guys handing out earplugs on the street corner, it was that loud. Fortunately, some areas inside the building where I gave my talk were relatively quite. The offices of some of the people I met were not so lucky.


In other news, I’ll be turning off the option to comment on this blog, even though I haven't received a single one yet. Call it a premptive strike. I visited another blog, and saw a whack of “comments” that were nothing but typical spam advertisements. Gah.

20 May 2004

When will they end?

I am still keping busy trying to finish projects that I seem unable to start any significant new ones.

For instance, I am still working on Search Committee stuff, trying to fill two more positions. We're arranging on-site interviews for two more candidates to come for the first week of June, with another one possible the second week of June. At this rate, the Search Committee work won't be done until the end of next month / early July.

I still have three of my four Honours students who have yet to hand in their final draft. One more should be done tomorrow, though.

And I still have analyses to do of my pilot project for teaching technology. And I haven't been able to find time to order teaching supplies for my summer students, which is surprisingly time-consuming. And then there are the manuscripts I should write, the grant proposals I should write... yikes!

I'm also trying to accomplish all this while I am simultaneously preparing to visit the Austin area on the weekend and early next week. I'll be visiting my colleague Virginia Scofield, then spending Monday networking with the faculty in the Section of Neurobiology, among others. I'm giving an informal seminar, so I'm prepping my PowerPoint slides right now.

People have been asking me, "Are you going to go back to Canada for the summer?" (or "on vacation," or some such). My stock response is to laugh and say, "I have real work to do."

19 May 2004

The big news

A few posts back, I hinted that there was some good news coming. Now, I can finally tell you what it was. Thanks to our College Dean, Mike Eastman, UTPA received a $1.3 million grant for undergraduate research from the Howard Hughes Medical Institution. The university even got mentioned specfically in the formal HHMI press release. (Edit: The success of this grant got noticed by the University of Texas Chancellor, who sent a congratulatory email to our president that is now making it down the line to me.)

I was involved somewhat in helping to prepare the grant application last summer (I mentioned it here), so I am hoping to reap some small benefit from it. Although a planned laboratory bus got mentioned in the press release, actually the bulk of what we'll be doing will be in the Biology and Chemistry Departments. We'll have undergraduate fellowships, a much needed seminar series, and undergraduate research symposium, and more.

I had a two-part response to hearing this news, when the Dean "leaked" it to me a little in advance. My first thought was, "Yes!" My second thought was, "How much more work am I going to have to do because of this?"

In the not so good news, the microelectrode puller request isn't going to happen, as the particular University fund I was hoping to tap into is supposed to be for equipment replacement rather than new purchases.

And several faculty in the Department had their requests for teaching release to do research turned down. I think this may be the first time anyone in the Department has had this request turned down. It's made for some very unhappy campers, and I can't blame them. It's a fast and efficient way to demoralize people.

In the better news department, I've submitted abstracts to give talks at two meetings. One in July at Western Nerve Net (the meeting I gave my first "pro" presentation at), and one in October at the annual Society for Neuroscience meeting. The Society for Neuroscience abstract is always a bit frustrating, because it has to be sent in so far in advance. You often have to something based on your preliminary data, and hope that they productive experiments you do in the intervening summer don't change the story too much...

12 May 2004


The first good news is that all four of my Honours students have successfully defended their theses, with my last student, Anna, doing her defence today.

I also got word that I'll be able to purchase a Sutter P-2000 microelectrode puller using money collected from a "technology transfer fund" students pay into. The reason I was able to tap into this was that I'm creating a new class, Neurobiology Methods, which is a lab course. It's been approved at the university level, but since nobody does anything remotely like this, I will need lots of equipment for the course. This was one of the bigger single purchases, and is a pretty pricy piece of kit (over $12,000!). I'll be able to put it to good use in research, too, when the class isn't running.

And I love the idea of having a piece of equipment with a laser capable of melting solid rock! (The puller can make electrodes out of quartz, and quartz is rock.)

07 May 2004

Three down, one to go

My Honours students Gloria and Marco both successfully defended their projects today in back to back presentations. Makes for a long day. It's just 4 in the afternoon, but it feels like it should be 6 or 7 in the evening.

Perhaps part of that fatigue is because today was the last official day of the semester. Marks were due to be handed in this morning, although I met my self-imposed deadline of getting them in at least one day early. I am now cast adrift, with no courses to teach for 3.75 months... to do grant writing and manuscript writing and supervising students on lab projects. Going to two more forums for candidates for a new university president. And let's not forget that there are three job positions that I'm actively trying to fill, in my role as Chair of the Search Committee.

The grapevine has it that there is good news for the University to be announced soon. I don't get to tell you what it is for a few days. But it's cool, and will be very helpful to a lot of people here.

05 May 2004

One down, three to go

The first of my four Honours undergraduate students, Nisha, successfully completed her defence today. Yay! Now, I just have to get three other students through their defences on Friday. And about a dozen other things to do by Friday, but oh well...

I also just put together a small request for a big piece of equipment: a microelectrode puller with a sticker price of almost 13 grand. We'll see how it goes.

03 May 2004

The beauty of data

I was analyzing some results from a simple little experiment that I had done. The picture below is a recording of neural activity in the tail of a crayfish.

Notice the large, regular spikes? They start slow, speed up, and then slow down again. Those are from a single neuron: the tonic stretch receptor of a muscle receptor organ. This is a little sense organ that detect bending in the tail: the more it bends, the faster the neuron fires spikes. I've shown a recording of them in this journal before, because they were the first neurons I was able to record from in my lab.

You can see there are a few other neurons firing in this trace: a few bigger, most smaller. Using the marvels of computer technology, I can sort all of those by shape so that I'm left with just the one cell I'm interested in. In practice, it tends to miss a few spikes here and there, but in this case, it did a pretty good job.
Now I can focus in on just the response of the one, single neuron I'm interested in, shown in red.

Because this neuron fires all the time when stretched very consistently, the major thing we're looking for is, "How does that firing rate change?" Yes, I can see it gets faster and slower, but I'd like a bit more detail than that. I plotted the instantaneous frequency of the firing rate (spikes per second, calculated spike by spike rather than an average).

And I was shocked by what I saw.

Clearly, this neuron didn't just speeding up and slowing down once. It sped up, then went slower and faster several times, resulting in these distinct peaks in the firing rate. It wasn't visible in the initial trace, but was blindingly obvious when you did this simple analysis.

The shock wasn't just over realizing that the neuron's spiking was a bit more complex that I first though; the shock I felt was the shock of recognition. I looked at those dots, outlining a shape with the distinctive series of "scalloped" edges along the top. I'd seen that shape before. I'd seen it a few times in a recordings I'd made myself during my Ph.D. work. Mostly I had seen that shape in scientific papers by other authors, like these two traces here.

From Figure 1 in Wiens, T.J. 1993. J. Comp. Physiol. A 173: 435-444.

What that picture shows you are intracellular recordings from two muscle cells. A neuron is being stimulated by the experimenter (Ted Wiens, in this case), and the muscle cells are responding to each little puff of neurotransmitter that the neuron releases. (You can tell it's an old picture by the grid of dots visible in the second trace. This was probably photgraphed straight from an oscilloscope, which usually had a little grid to help you measure things. This was back in the dying days of analog neurobiology, before computers were fully integrated into neuro labs.) What's shown here is the muscle cells electrical response, but the amount of contraction -- the tension -- created by that muscle cell will closely parallel the electrical activity. Each peak of the trace above is the muscles response to a neuron firing once (in this case, the motor neuron fired four times).

But I wasn't recording from muscle. I was recording from a sensory neuron.

I put together what this trace was showing me in a flash. Somewhere in this preparation, a motor neuron was activated and firing action potentials. In fact, it's probably just a one motor neuron, because crustacean muscles have very few neurons to control their muscles. The motor neuron is firing, the muscle it's connected to is contracting. These little muscle twitches cause just a little tiny bit of tension, so slight that you can't even see the tail moving in the dish. But it's moving the tail just enough that the stretch receptor is picking up the tension, and reflecting the muscle's activity in its firing rate.

It was beautiful.

And because beauty should be shared, I went looking for someone to share it with. Because it was Saturday, not many people were in there office, but poor Chris had to bear the brunt of me geeking out over this trace. I did not feel guilty about this, since he was pulled me into his office and was waxing rhapsodic about some plant rust (fungal infection) or something a few days before.

It's beautiful to me not because it's any great discovery. I mean, neuron fires, muscle twitches, sensory system tells you "muscles twitching" is pretty basic stuff. No, I think what's beautiful is to see so directly this sensory neuron pick out what are, in all likelihood, the activity of single motor neurons is amazing to me. That, and the experience of looking at the data, having that rush of recognition and almost immediately knowing what's going on... It's exhilerating. It really is. It's pretty much what we scientists live for. Admittedly, we hope that sometimes it's on a larger scale: bigger data sets, more important experiments, things that push the envelope of knowledge, and so on. But even little moments like that are pretty special.

After the intital rush, I became interested in why this experience was so strong for me, and I think it has a lot to do with the immediacy of what I went through. I plotted the data, recognized the shape, and had an explantion in the space of a few seconds. I think this demonstrates just how important exploring and visualising data is. I'm a real admirer of Edward Tufte (last name pronounced "Tuft-ee"), and he talks a lot about this in his works. I wonder how many discoveries have been lost over time because people didn't have the right graph. For example, in this case, I was able to immediately recognize the shape because of the particular plot I chose. What if I had plotted the frequency not spike-by-spike, but averaging the firing rate every 0.1 seconds instead?

I don't find this graph as pretty as the one with just the dots, but I probably still would have recognized the shape. But what if I averaged the firing rate over every half a second instead of every tenth of a second? I would have seen this...

Clearly, a lot of information's been lost. I can tell something is contracting somewhere, but I can't see the exquisite sensitivity of the stretch receptor and how closely it seems to be tracking the muscle tension. So sampling at a higher frequency is better, right? Not necessarily. The original line graph (two above) took the average every 0.1 seconds; the one below takes an average every twentieth of a second...

Ack! That is one ugly graph! I might have recognized what was going on here, but I strongly doubt that I would have come to the conclusion that what I was seeing was beautiful. Even if I changed the line colour away from that gaudy pink.

And if I had plotted the exact same data not as a dots or a line, but as a bar graph of spike counts, I doubt I would have drawn any conclusions about what was going on besides the obvious (the neuron fired faster, then slowed down).

Incidentally, this is the same sampling rate as the first of the "pink line" graphs above: counting spikes every tenth of a second. Yet in one case, the graph reveals; in another, the graph conceals.

There are several lessons here. This example shows that creating a good graphic of the data is not a straighforward thing. "Show me the data" is a constant refrain among experimenters, but there will always be multiple ways to do that. If you don't take care in representing that data, particularly graphically, you will miss evidence for some very interesting things. And it also speaks to why a really good graph or image is so powerful: the immediacy. In this case, it was allowing me to see, in a measure of rate of one neuron, to trace the activity of two others -- and to see it, graphically, as clearly as if I had recorded from those other two cells.

Science is often about simplicity: the simplicity of realizing that what you thought were two different things are really the same thing. And I think that is why I experienced this small little set of nothing data as beautiful: in examining one thing, I saw another.

02 May 2004

Living cliches

So I was at work this morning, had set up a time to meet my SO and was running a wee bit behind. On the way back home, ran into two of the Biology student. One said held out some flower and said, "What's this?

"A plant," I replied (well, it was).

She asked me to smeel it and I said no. She said, but it smells nice, and I said I was kind of late and had to go.

"So you're too busy to stop and smell the flowers?" she said.

My life in a nutshell.


Next post: an essay on the beauty of data.