As I wrote about before, my semester lab project for neurobiology has to do with regeneration. The idea is to damage the spinal cord and observe wonderful regeneration. This proposal was based on some articles I read about regeneration of zebrafish hearts, fins, tails, etc. Unfortunately I haven’t had much luck so far.

Last week, armed with an exacto knife, I performed my first round of spinal cord butchering on fifteen zebrafish that were only a few days old. The zebrafish are captured with a glass pipet and then immobilized using auger that’s just warm enough to be in liquid phase. They are then mounted on a slide under the stereoscope. I quickly discovered many faults in my methods, one of which being that I captured the fish in too many drops of water so when the auger was added in a test tube, the fish weren’t completely immobilized. I would then carefully approach a fish with the exacto knife on the slide under the scope and it would turn into a bucking bronco. Eventually I perfected the art of capturing the few day old zebrafish with the pipet and putting them in test tubes in only one drop of water, thus partially solving the immobilization issue.

The second problem I encountered is that there is nothing exact about an exacto knife under a stereoscope. Accomplishing this spinal cord severing is much like peeling an orange with a baseball bat in that it’s extremely difficult without making a mess. Even with the fish immobilized the tail doesn’t really stay put when pressure is applied with the seemingly crowbar sized exacto knife. The key to this dilemma, although I have yet to master it, is probably making the layer of auger on the slide as thin as humanly possible so that there isn’t as much room for movement.

All the zebrafish from my first attempt died. Two of them were alive for a day or so but barely. I did another round of zebrafish butchering with fifteen more fish yesterday (yes I enjoy spending my Sunday afternoon in the neurolab) and from what I could tell, all but two of them died immediately. I’ll have to see if the elite two are still swimming around today but if not, I’ll try yet another round of fifteen and see how it goes. If anyone has any ideas for instruments or methods that could improve my success, feel free to insert a comment.

In preparation for my trip to the Caribbean next semester, I spent this weekend taking a class to learn how to SCUBA dive. My class and I learned all about the necessary equipment, what to do in emergency situations, and how to stay safe while SCUBA diving. We also learned about the physics of pressure, volume and density, so that we could better understand what happens when you descend into the deep. This inevitably led to a conversation about Nitrogen narcosis.

Nitrogen narcosis, or “rapture of the deep”, is a condition in which the symptoms resemble those due to intoxication by alcohol. Divers experiencing nitrogen narcosis lose their decision making abilities, their focus, and their judgment, coordination and multitasking skills become impaired. What could this potentially mean for the diver? They could ignore safe diving practices because they feel invulnerable to the dangers of their surrounding environment (sounds a bit like the actions of those individuals who are intoxicated by alcohol).

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Synesthesia is going to be the discussion topic for our upcoming neuroslam in two weeks. Synesthesia is the rare ability of a select few individuals to see numbers as colors or as in the article that I’m preparing to discuss (Hubbard 1996), experience varying degrees of light and dark as melodic intervals. The observed pattern is that individuals experience lower pitches or descending melodic intervals in correlation with darker stimuli and higher pitches or ascending melodic intervals in correlation with lighter stimuli. The important detail about synesthesia is that individuals experience it involuntarily whereas most individuals without synesthesia can choose to consider a set of stimuli using a secondary sense that they normally wouldn’t.

One of the experiments discussed in this article was conducted with undergraduate students coaxed into participating with the offer of some credit for an intro to psychology course. The students were placed in front of an Apple RGB color monitor and grey squares of differing light intensities were presented in conjunction with a perfect fifth for four seconds. Eight perfect fifths were used, each beginning on a different tonic and thus each having a unique frequency. The squares were presented on either a white or black background. The students then rated how similar the square and the interval were on a scale with one as the least and nine as the most. One of the questions considered with this experiment is the effect of contrast between the background and the grey squares on perception.

A second experiment was set up similar to the first experiment except that students (who had not participated in the first experiment) were presented with an interval at one of the selected frequencies and asked to choose among several light intensities of grey which correlated best. Correlating one perfect fifth to a light intensity that was presented with multiple light intensity options successfully diminished (no pun intended) the effects of background contrast on perception.

I thought of some questions when I was reading this article and then afterward studying for music theory. Are there individuals who experience synesthesia such that they correlate varying degrees and intensities of lightness with more complex types of music intervals? Do minor or diminished intervals correlate to a different light intensity than major or augmented intervals? What about different intervals of the same quality? Do ascending minor sixths correlate to a different light intensity than ascending minor thirds? If an individual with true synesthesia enters a concert hall do they experience sensory overload? (just kidding) I’m sure one of us neurobio students will post about neuroslam in a couple weeks to fill everyone in on our discussions but until then there is a lot of good reading on the subject.

References:

Timothy L. Hubbard. “Synesthesia-like mappings of lighness, pitch, and melodic interval.” American Journal of Psychology. 1996. v109n2: p219

It’s puzzling: he’s a rich and successful engineer, but I don’t see any particular virtue to his participation at SfN, and judging by these remarks, he just exposed himself for an ignoramus.

During the time Andrew S. Grove spent at Intel, the computer chip company he co-founded, the number of transistors on a chip went from about 1,000 to almost 10 billion. Over that same period, the standard treatment for Parkinson’s disease went from L-dopa to … L-dopa.

Grove (who beat prostate cancer 12 years ago and now suffers from Parkinson’s) thinks there is something deeply wrong with this picture, and he is letting the pharmaceutical industry, the National Institutes of Health and academic biomedicine have it. Like an increasing number of critics who are fed up with biomedical research that lets paralyzed rats (but not people) walk again, that cures mouse (but not human) cancer and that lifts the fog of the rodent version of Alzheimer’s but not people’s, he is taking aim at what more and more critics see as a broken system.

The institution of research in this country isn’t without its flaws, but Grove doesn’t have a clue. There are two big reasons we can’t just ramp up biomedical research and see new results flowing out of the pipeline and into the hospitals at an accelerated rate. The biological research program is not comparable to Intel’s computer chip production!

• Biological research is not an exercise in applied engineering — we’re trying to discover fundamental unknown elements of biology, and it isn’t at all like scaling up or refining chip production. This is important: you can’t make science a process of applied engineering without destroying it. The job of the scientist is to uncover whole new principles and concepts, and that means there is a lot of scurrying about to reveal stuff that isn’t immediately obvious how it can be used in a practical sense.

  Grove is looking in the wrong places. We’re seeing rapid progress in many fields of science — evo-devo, to name one close to my heart — and he’s simply blind to them, and demanding immediate productivity in areas where he can’t even define the problem and which need more basic research to improve our understanding.

• I would be more impressed with the superiority of engineering in the L-dopa example of Grove’s strategy for improving a chip didn’t involve throwing out the old model and plugging in a new one. Why didn’t Intel develop a treatment for my old 8088 that would transform it into a quad-core 64-bit Xeon. One could argue, I suppose, that our comparable strategy for Parkinson’s is to allow the old relics to die off while our Uterine Fab Units build brand new brains that work without crashing.

  It’s especially ironic since he is demanding new treatments because he has Parkinson’s, and now he thinks he can just demand a cure on a schedule, like he was ordering an iPhone.

It’s too bad Grove wasted all those years playing with simple toys like microprocessors instead of trying to understand something rather more complex.

I really do have no sense of shame, and since Halloween has just gone by, I have even more opportunities to pander to the cute. How about a dog?

Or how about … adorable little kids?

Have no fear, the conference ends today, and I’ll be turning off the saccharine drip.

While I would love to devote all of my time to neurobiology, I do have other classes that require my attention. In one of those classes I am writing a research paper on tuberculosis. While researching tuberculosis I began wondering if there were any strange cases where tuberculosis has neurobiological effects. A google search brought me to this article. While this is not exactly what I was looking for, it did pique my interest. It seems like drugs taken for one thing end up treating another as well. In Biochemistry we recently had to read an article about how the obesity drug Orlistat is a possible cancer treatment. I just wonder how people first begin to realize that a drug taken for one thing affects other areas as well.

So while most of my fellow undergraduates were leaving town to go somewhere, anywhere, other than Morris for fall break, I had to stay behind. Sure, staying in Morris is not really all that bad, I mean, some people actually live here (sorry Professor). But I will be honest-it really is not on my list of top places to live. It is just, well, boring. I had to stay behind because I had some animals I had to take care of, and I will admit, I was looking forward to spending time lying in bed, working with my horses, and catching up on my senior seminar. Little did I know exactly how much time I would spend doing the first, and hardly any of doing the latter two.

Yep, this break I got floored with a virus. AND I literally mean floored. We shall call it the flu, because I had all the flu-like symptoms. Headache. Swollen lymph nodes. Achy neck and back. Fever. Achy stomach. Dizziness. So I spent a wonderful Saturday doing all the things a person my age would love to do, and then spent Sunday, Monday, Tuesday, Wednesday and some of today confined to my bed. Sure, you can say,

well you slept through most of it, so it couldn’t have been all that bad

But believe me, what little I was awake for was horrible. Mostly because it was absolutely gorgeous outside, I didn’t have any classes to attend, and yet my body was waging a war inside of me.

So, I understand the basic principle of how viruses work, but how can one virus have a multitude of diverse symptoms? What’s with the headache, and the achy joints? Do viruses affect neurons the same way they can affect other cells? Do they even invade neural cells?

The beginning of this week was fall break at our college campus. We had the weekend off as well as Monday and Tuesday. Since I had been planning to return home to northern Minnesota for the first time since moving down to west central Minnesota in August, I decided to take Thursday and Friday off also. The few days I spent away from this desolate prairie wasteland and back among the conifers and lakes were phenomenally enjoyable.

This is my first year of college away from home and a long way from home it is. I remember the first few weeks I was down here, only vaguely though, a lot of adapting has taken place since then. The three-day dragged out orientation process for freshmen and transfer students at the end of August was intensely boring. I had been informed by mail that my presence was required but it would have been great had I known what it entailed and that I very well could have gotten away with not attending (this sounds negative, I know, but I’m sure some of you can relate). I remember the immense amount of time and effort it took to meet new people and figure out who to make friends with. Luckily the homework load had not picked up yet and there was plenty of free time to devote to this. Did I mention I had never bought my own groceries before coming to college? The first night I went to buy food I had no idea what I needed to sustain myself in a semi-healthy manner. The first five items I put in my basket had something to do with hotdogs. I’ve since learned a few things about grocery shopping and cooking. Although the first weeks were uncomfortable and sometimes frustrating, it was well worth the effort to take them on.

The drive home was long and rainy. There were a few deer that crossed as I approached them but staying attentive kept my vehicle intact. My lily plant sat quietly on the front passenger floor and when I inadvertently opened the glove box on its head I caught myself apologizing. Talking to a plant seemed odd to me so I ignored it and its personal temperature preference for the rest of the trip.

When I finally got home just before midnight, I sat in my living room with a bowl of soup, quietly but excitedly looking at everything I hadn’t seen for a while. The pictures hanging on the wall, the bookshelf filled with various things, the scent of my dad’s cooking brought forgotten memories rushing back to me. The plant atop the bookshelf with vines that had hung down half way in August had now reached the floor. My dad, who was sitting in his recliner on the opposite side of the room with his own bowl of soup, talked about things that had happened while I was gone, the new addition on the back of the garage, why our silverware was different, and how my aunts and uncles are doing.

The weekend flew by quickly and before I knew it I was sitting in neurobio again yesterday morning (we have wednesday discussions in the cafe now so PZ can get coffee). The time I spent among the seemingly infinite number of trees and lakes in northern Minnesota was enough to keep me going until I can go back again. For now it’s just good to know that everything I call home and everyone who means the most to me are still up there, safe and sound.

… well not today. I learned very little today , but generally, here are some interesting things I’ve picked up in class:

-If you sever a cat’s cerbral cortex from its hindbrain it can still walk on a treadmill (in a harness that compensates for the poor feline’s lack of balance). This was the topic of one of PZ’s many tangents.

-One way to inhibit the HIV virus is to make a drug that targets a protein our cells make. The key is to identify a protein the virus needs but that we do not. CYC202, a cyclin-dependant kinase inhibitor, may be one such drug.

-“HIV virus” is redundant, but hey, so is the genetic code.

-If you race flatworms in a maze, grind up the fastest ones, and feed the product to flatworms having yet to try the maze, you might find that they run the maze faster than their non-cannibal counterparts. Of course, you would consider that flatworm may simply be highly nutritious, because you’re a scientist, and that’s what they pay you the big erlenmeyers for.

-Badger culling. That’s right. Badger. Culling. It’s used to decrease badger/cow contact in Great Britain as badgers function as a bovine tuberculosis infection reservoir for cattle.

-EtOH and H20 are miscible. Whew… and to think I almost made myself an acetone martini…

Squeeeee! I like totally love Robert Hooke, and now you can read Hooke’s notebooks online. The broadband version is phenomenal — it’s like leafing through the 17th century.