Category Archives: animal research

Dear lord…

So, the hell that has been my thesis proposal is essentially over. Getting mine approved took a few weeks longer than usual because I got FUCKING SANDBAGGED BY MY GODDAMN BOSS DURING MY PROPOSAL. But whatever, I’m (somewhat) over it now that I have a project that’s been approved by my committee. The project is damn near impossible and almost certainly not going to work, but it’s better than not having a project. I’m still going to have to throw out 8 months of research, but I still think things could somehow be worse.

For the first time in years I’m actually making time to have fun and meet people. I’ve been going on freaking boatloads of dates the past two months and am loving the chance to go out and meet new people. I do feel somewhat bad for the first half-dozen or so of the women I went out with since I was still just working out the awkward out of my system. Never going on a real date as an adult will do that to you. I was FULL of awkward. Like, to the brim. Okay, not that bad, but it wasn’t pretty. Sorry, first six or so ladies, I really am.

But even though research isn’t going well I’m not letting it bring me down since life in general is actually quite enjoyable. I still have a few friends who either can’t or won’t see the world this way and that is really beginning to rub me the wrong way. I’m just now beginning to realize that happiness is largely a choice for those of us fortunate enough to be in our situation. I mean we’re doing bleeding-edge medical research at one of the best freaking labs in the field, in one of the best cities in America, and we’re getting fucking PAID to get our degree. This is, of course, a very rosy view of our current situation, but it’s one that helps change a possibly shitty situation into one that is at least tolerable.

So, life is decently good and I’m happy. That is all that really matters right now.

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Filed under animal research, crazy, grad school, just sad, life, neurobiology, sleep deprived

The grad school blues

A large portion of grad school is reading. Lots and lots of reading and doing what you can to synthesize the information into a whole and then do something with it. This is much more difficult than it may seem for a plethora of reasons, but when it really comes down to many areas of the literature the larger picture makes sense. Things are somewhat ordered.

This is not the case with the literature I’m reading for my project. The area I study seems to be nothing but a clusterfuck of randomness. However, the data is rarely presented this way which makes reading the papers that much more difficult. For instance, I just read a paper that had a very nice looking bar graph, but after reading the text I realized the data for that figure was only from ~15% of the cells they recorded from. I’m not saying that making the comparison they did wasn’t valid, it was, but it was also somewhat misleading since you kind of had to dig for the rest of the story.

This is really bringing something to light that I wish more people in my lab (really, just some of the higher ups) would recognize: the nucleus we study IS NOT HOMOGENOUS. All the cells share some basic characteristics, but that does not mean we can treat them as a homogenous group like we do. I’ve been fighting this stance since the beginning due to the literature and my own findings and while I seem to have convinced my peers the higher-ups still don’t apparently see it that way.

Science can be frustrating.

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Filed under animal research, biology, disease, grad school, neurobiology, parkinson's


Turns out that going without internet still sucks (I did this a few years ago when I first split with my wife), but going without gas is even worse. Yeah, the morons from the gas company shut my gas off instead of beginning to charge me for it. I knew they were dumb, but this has been going on for a week now and I’m getting real sick of it. Cooking is my stress relief, so thank god there’s very little stress in my life right now

On a more positive note the divorce paperwork is all filled out and ready to go. Turns out it’s just checking a few boxes and signing your name about a dozen times (as long as you’re getting an awesome divorce like my wife and I). Have to say it looked much more intimidating than it really was.

My apartment is coming along nicely since I got my bed on Friday. I’m at work now, but when I get back I plan to put up a bunch of pictures and paintings and really help make my place feel more like my home. Still need to get rid of those boxes though…

And science-wise things are progressing quite nicely. This Thursday will be a trying time since the mice I injected with Channelrhodopsin will be ready to use and, fingers crossed, I get a boatload of data. In theory I can knock out all the data I need with just a few healthy animals with unique injections. It won’t work out quite that nicely, but I still have hope that all my training will get me through this.

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Filed under animal research, biology, divorce, grad school, life, marriage, neurobiology, parkinson's

Neurological disease: a complicated beast

Earlier today I was doing a little Googling looking for information that I plan to use for a thesis project when I came across a blog about the science of Parkinson’s Disease. At first I was really excited since I rarely see blogs about the science of specific diseases and I feel those are very much needed in today’s serious state of scientific misinformation. After the initial surprise of its existence, I actually made the mistake of reading the blog. I was not only disappointed, but saddened as well.

My disappointment was less about the apparent state of research and more about how research (and researchers) is presented to patients and their families. How and why biological research is conducted is largely a mystery to the vast majority of even the most educated people. What disappointed and distressed me most was how research was perceived by this patient. It was of the “why aren’t you doing this?” mentality that I find is quite pervasive in online patient communities of all diseases I’ve come across. This idea that we researchers are not really interested in certain questions about disease progression and pathology are partially correct but largely misguided, and often perpetuated by the perceived lack of progress in curing the disease in question.

It is true that scientists often halt seemingly promising lines of research much to the dismay of patients suffering from a debilitating disease, but it is not because we do not care. Instead, we do it because it makes sense scientifically and financially. If it doesn’t seem to be a fruitful endeavor then there is no point to keep wasting very valuable time and money pursuing it. There is also a simple reason we do not let patients dictate our research direction: they do not understand the science behind their disease. This is not an insult, but a simple fact. These are very complicated matters that take years of training in order to just begin to understand, and to expect a patient with little knowledge of biology to truly understand the research is unreasonable. That is why we don’t expect them to understand the underlying pathophysiology of their disease. However, patients oftentimes feel they understand more than they do (a little bit of knowledge…) due to their intimate knowledge of their disease. I cannot blame them, but I do wish they would have a little humility and acknowledge that there are plenty of professionals out there who have studied their disease for years in order to understand and, hopefully one day, conquer it.

Though most of us scientists got into research due to simple human curiosity it does not mean we don’t care about the real world implications of our work. We’re working hard not just for ourselves, but also because we know it makes a difference not only in the lives of patients, but also other scientists, and humanity at large.

Overall, I wish the author of the above blog the best in his/her treatment and that this post may help explain a bit of why we do what we do, but I also wish that some of the opinions of the author are changed for the better.


Filed under animal research, biology, cancer, disease, evolution, grad school, huntington's, medicine, morality, neurobiology, parkinson's

A day “off”

I’m taking a day off.

Well, kinda. I’m staying home, but I’m still working so it’s about as close to a day off as I’ve had in the past year. It can get crazy in the lab and I can end up being so distracted that in the ten to twelve hours I’m there very little actually gets done. Also, I’m getting burnt out due to the stress of science.

Ever wonder what a scientist does? Then I’ll tell you (I’m assuming you said “yes”).

These days science is highly technique heavy which means two things. One, the research is incredibly interesting and typically quite solid. Two, there is loads of failure and data interpretation can be rather difficult. A relatively common technique we currently use to understand neurons is called patch clamping for reasons that will shortly become obvious. Exactly what I do is called slice physiology since I’m patch clamping in a thick slice of brain. Anyway, let’s get to the technique.

We take a mouse/rat and deeply anesthetize it, then pump a very cold, oxygenated saline solution into the heart to perfuse the brain. This step serves to rid the brain of blood and rapidly cool it to ensure minimal death of the tissue. We then remove the brain immersed in the cold saline solution, glue it to a pre-chilled metal plate, and then place that metal plate in another pre-chilled basin filled with the chilled saline solution. We then use a machine called a vibratome to cut “thick” sections of brain tissue between 250-350 microns thick (roughly the thickness of 3-4 slices of standard paper). We collect those sections and place them at an elevated temperature to help them recover from the trauma induced by the slicing. The whole process takes about an hour.

After 30-40 minutes at the elevated temperature the slices are ready to use. We place them under a microscope and visualize individual neurons that we will want to record from. The rig we use is actually quite impressive looking (an example) and we get images that look something like this.

And that’s something similar to what you SHOULD see. If that’s what you see then your job is easy and you can go ahead and get nice recordings easily (which is what that blueish thing coming from the left of the image is doing). However, the image above is from a very young animal and is of an area that is very easy to visualize, both of which lead to clear images and relatively easy experiments. I have to use six-month old animals (cells die extremely easily) and record from an area where there are so many neural fibers running through that it’s difficult to see anything, meaning that even my best days suck. Yesterday I just couldn’t take any more of it. Four straight hours of trying to get a decent cell and I may have gotten one.

I wanted to kill someone. That’s why I needed a day off. I deserve this.

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Filed under animal research, grad school, life


I’m fairly well versed in biology, and what I don’t know I can look up and not be confused by the jargon.  So, I have a question to anyone reading this: any questions you have about anything biology (or general science) related that you would like answered by a scientist?

Something you read in the news or a magazine about recent biological advances sound fishy and want to get the to bottom of it?  Ask me.

Hear your dad spout some craziness about one of his “theories” and wonder if it has a grain of truth?  Ask me.

Ever wonder why you have a blind spot in your eye?  Ask me.  (hint: if there’s a god, he’s retarded)

Wonder why researchers still have to kill tens of thousands of animals a year in order to do necessary research?  Ask me.

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Filed under animal research, medicine, morality

Science: it does more than you think

One of the main questions I get about doing biological research is: so what do you actually do?  If my answer isn’t “I’m trying to cure Parkinson’s/cancer/some other disease!” I tend to get one of two responses.
1. Why aren’t you trying to cure (insert disease)?
2. (blank stare)

I don’t blame people for not understanding why I do what I do.  Considering billions of taxpayer money is spent every year on basic research I can see why the general public wants to see tangible results in the form of new drugs and therapies that can help people with debilitating, and often lethal, diseases.  This is why I do everything I can to inform anyone who is willing to listen about the joys and benefits of basic research.

I’m going to gloss over a lot of details, but you have essentially two kinds of research: applied and basic.  Applied research is a program where a finding (lets say a new class of antibiotic) is used to find a direct application that can benefit people.   In the antibiotic instance it would involve first using the new antibiotic on cultured bacteria alongside standard treatments.  Then you move on to animal models and, if it all works out, to clinical studies in humans.

Basic research is, well, for lack of a better term, more basic.  I know you can’t define something by using the very word you are defining, so let me expound on this a little bit.  All basic research is goal oriented in a sense, but the overall goal is much more open ended than that of applied research.  We basic researchers try to figure stuff out just for the sake of figuring it out.  Yes, it may have a practical application down the road that we’re kind of, slightly, interested in but the main goal is to expand humanity’s knowledge base so that even more discoveries can be made.  The key to basic research that everyone should understand is this: no one knows what piece of knowledge is going to lead to useful, practical applications.  Just because we’re scientists doesn’t mean we can see the future.  We make educated guesses based on what we currently know to try and narrow down future possibilities (and we’ve become quite good at that), but we’re far from perfect.

One of the best examples I have ever seen of a basic research finding having profound real-world implications is the discovery of a simple little protein called ubiquitin.  I heard the story of it’s discovery when I attended a lecture by Nobel laureate Aaron Ciechanover (yes, I had to mention that) and it was essentially this: scientists didn’t know anything about the possible breakdown of proteins in the body at the time, so Aaron and a few others decided to look into it.  There were plenty of theories about what was happening to these proteins, but no one had any solid answers.  Turns out, the protein ubiquitin is critical to the specified destruction of proteins, and when this system gets fucked up, you get fucked up.  However, now that we know what the system does and (mostly) how it works we can now look for drugs to target particular aspects of this system to cure diseases!  Exciting, I know!  But, if the basic research hadn’t been done we would instead be blindly looking for drugs, and even if one were found we wouldn’t understand how it works or interacts with other parts of a system.

These discoveries happen all the time.  Occasionally they directly help humanity, but I would argue that in all instances they, at the very least, indirectly help.

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Filed under animal research, medicine