The holiday season is upon us, and our source of cocoa is going on strike. I hope the US Strategic Chocolate Reserve is well stocked, or Santa will go into withdrawal this Christmas eve.

(We ‘podmas celebrants have no worries, at least, unless the herring supplies are depleted.)

Here’s a horrible story: a man who bears a grossly disfiguring tumor on his face, one that threatens his life and has afflicted him since adolescence, is only now considering surgery to correct the problem.

Why not before? Because it might require (and now definitely would require) blood transfusions. And he’s a Jehovah’s Witness. You have to wonder what wretched, evil excuse for a human being among his church associates has been telling him that he shouldn’t get this life-saving surgery because God wouldn’t like it.

This week is the second to last week of the semester before finals and everything is coming down to the wire, including my neurobio lab project. PZ was so kind as to come in and help me out this past Sunday morning; the morning after the blizzard had quieted leaving everything covered in various quantities of snow. In going over my methods we found that I wasn’t adding a drop or two of water on top of the auger layer with the immobilized zebrafish. The reason this is important is that so after the spinal cord severing is accomplished, the auger layer is separated allowing water to surround the fish immediately and preventing air exposure. The fish can then be pipetted up and put into a dish of water for observations. PZ also suggested using water with an increased concentration of calcium (14g/100mL) to facilitate better fish recovery. The fish should not be left however in the calcium water for an extended period of time because it can adversely affect development.

Repeating my methods and taking into practice the slight changes that PZ recommended, I found that after one day, four of eleven fish were still alive! After slicing up more than sixty fish with a 100% mortality rate after one day and wondering what on earth I could have been doing wrong, I was ecstatic. It’s unfortunate that this success has come so late in the game and the writeup for this project won’t show much for results other than how not to butcher zebrafish. I have learned quite a bit though about the interesting techniques I’ve been using and also about the differences in zebrafish at various stages of development. So with that, back to the lab I go to continue working with zebrafish.

As I’ve mentioned before, my class has been reading Time, Love, Memory: A Great Biologist and His Quest for the Origins of Behavior^{(amzn/b&n/abe/pwll)}, which is in large part an account of the amazing work Seymour Benzer accomplished over the course of his long career. Now I’ve got sad news to break to the students tomorrow: Seymour Benzer has died at the age of 86, after a long and exemplary career as a “scientist’s scientist”.

The seed of this mornings discussion in neurobiology was “Time, Love, Memory” by Jonathan Wiener. As has been the norm in past weeks we met in the on campus cafe bringing along with us four insightful questions each to keep the discussion rolling along throughout the hour. Wiener describes later in his book (p192) the three necessary components of living clocks. Living clocks are the basis of circadian rhythms and must have an input pathway so that the clock can be reset by the sunrise and sunset. A good example of why this is important is that humans actually have a twenty-five hour clock that resets itself everyday to correlate to the actual day length of twenty-four hours (23 hours, 56 minutes, and 4.1 seconds for any physicists reading this). People who are blind or people who are not exposed to the sun at all will exhibit a twenty-five hour clock, out of synchronization with the earth’s rotation.

So my question was about animals that live near the poles. How do polar bears or lynxes reset their clocks in the arctic summer when the sun doesn’t set? Some thoughts were that perhaps the living clocks are reset by magnetism but quickly realized that there is no shift of magnetism that corresponds to the length of a day. Another thought was that if it’s always light out, does it matter when the polar bear sleeps? The polar bear could have a period of activity, followed by a period of decreasing activity, and then rest and sleep. Lynxes often hunt at night and rest during the day but if it’s always light out does their clock remain synchronized with the earth’s rotation? PZ mentioned there isn’t much research pertaining to this but If anyone knows of any interesting papers that would enlighten this topic post them up.

References: Jonathan Wiener. “Time, Love, Memory.” Vintage Books, A Division of Random House, Inc. New York. 1999.

Researchers at Cambridge conducted a study that measured cognitive function and analyzed images of the brain in individuals with obsessive compulsive disorder (OCD). Magnetic resonance imaging (MRI) was used to capture images of each participants’ brain, and computerized tests were given to study the ability of the individual to stop repetitive behaviors. Also included in the study were healthy family members of the individuals with OCD, and healthy, unrelated individuals used as a control. The family members were included so that the genetic link behind OCD could be explored.

The researchers discovered that individuals with OCD and their relatives did worse on the computerized tasks than the healthy control group. When the MRI photos were analyzed, individuals with OCD and their relatives were found to have distinct patterns in their brain structure, namely a decrease in grey matter in brain regions associated with the suppression of responses and habits.

It was noted that this decrease in grey matter may contribute to the characteristic compulsive and repetitive behaviors associated with OCD. However, researchers are still a long way from discovering the genes involved with OCD, and further research needs to be done to explore why some family members with the altered brain structure do not develop OCD.

Since the family members have similar brain structure, there must be something else contributing to the development of OCD. I wonder if there is something going on inside that is causing a chemical imbalance that contributes to OCD, or if environmental factors are important in the development of OCD. It would be interesting to look at identical twins and see what the pattern of OCD is in them.

This is why we need to keep a few philosophers around: they can succinctly name the logical fallacies committed by a certain cosmologist.

I once overheard an interesting confession from a friend of a friend. This guy had been drinking and was admitting to his buddy that he just wanted to get into a fight, punch the next person that walked through the door, stir things up. That sort of thing. I complained to my companion that it was precisely this attitude that causes so much conflict in society and, though my friend agreed, he sheepishly added that sometimes he too enjoyed the thrill of physical violence.

I was reminded of the incident recently in a class on the origins of aggression when we read a passage from Journalist Bill Buford’s Among the Thugs. Buford spent eight years documenting violent episodes in sports crowds and riots. He wrote of the intensity of a violent experience:

I am attracted to the moment when consciousness ceases: the moments of survival, of animal intensity, of violence, when there is no multiplicity, no potential for different levels of thought: there is only one–the present in its absoluteness

If we really can find a sort of solace, release, or even satisfaction in violence, I think this says something about our race, and it makes me wonder if peace is really attainable. We may find it difficult to identify with violent people as we are now, but how would we react if a loved one were taken from us? Would we want revenge? Maybe revenge is the search for the relief that violence can bring however transient or ultimately tragic.

Check out Deltoid for a set of refutations of common global warming denialist arguments. Then you can whine on that blog. (this thread is at 1146 comments right now—I think the blog is full, time to move on.)

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.