Okay, we all know this feeling - Sitting in a class you're totally familiar with, looking at the person presenting, hearing the discussion of our peers, and still thinking, "What is even going on." (Personally, once I've reached that point, I'm no longer asking it as a question - It's a statement of just how dumbfounded I am in that moment. I just keep taking notes and figure that at some point I'll be able to review, ask questions, and eventually understand.)

Now imagine taking away the familiarity of the content, and just add the fact that you are madly curious about what's going on around you. While that is generally me most of the time, this class really exemplified that feeling.

Today Krista and I walked from the lab to her Neuroscience class - but it's not what you're thinking of as a general "class" - there were six students, one intern, and a professor who knows how to present a great scientific debate. 

The class was structured around four papers - two read and presented by Alison (a student in the class), and two read and presented by Krista. These papers focused on a great debate of Neuroscience - Does LTP occur in the pre or post synaptic cleft? I think I know what you're thinking... What in the world is an LTP, why does it occur and are the post synaptic clefts the where of this question? If this is what you're thinking, you're on the road to being where I was at the beginning of the class, and in reality... all signed pointed to confused.

Just to give you a quick heads-up on where we're going, here's a few pointers on the vocabulary of the seminar:
LTP: Long-term Potentiation... Krista defined it for me as "the closest neural correlate of memory that we have, but it doesn't actually explain 'memory.'"
GABA-R: Inhibition channel for Chlorine (Cl-). 'R' just stands for "receptor." So we'd call this the "Gaba Receptor"
NMDA-R: Glutamate-binding receptor that Sodium flows through when the cell is depolarized.
AMPA-R: Another glutamate receptor (which is not one that Sodium flows through).

If you're still confused about what a synaptic cleft is, imagine your neuronal anatomy. Starting from left to right we have dendrites, which are attached to the soma (or the body) of the neuron. Currents travel down the axon where they reach the presynaptic cleft - where signals will be sent from in a synapse. The dendrite of the next neuron which will receive the message (sent from the presynaptic cleft) is called the post synaptic cleft.

In the simplest terms (and from my best understanding) a range of neuroscientists in the 1900's posed the question of wondering whether LTP occurs in the pre or post synaptic cleft... And, as all researching scientists would, they designed experiments to test their hypotheses. Although it seems like a "left or right" question, what I learned from student response yesterday as well as my own experimental and research based experiences - science is never simple, and science is never 'just' left or right.

So a number labs interested in finding an answer to this question conducted a various range of experiments based around their knowledge of neuronal receptors (those GABA, NMDA, and AMPA receptors we talked about earlier)... and although one scientist seemed to present research that leaned towards LTP occurring in the presynaptic cleft, the rest of the research was overwhelmingly leaning towards the post synaptic cleft... That's where things got interesting in our class...


At the end of both Alison and Krista's presentations, the professor asked the seven of us whether we thought LTP was presynaptic or post synaptic. "Presynaptic," he said. No one raised their hand. "Post synaptic," he said. (I reluctantly raised my hand  about 2 inches from the desk so that if I was wrong, I could make an excuse that it was just a twitch or something.) "Really? No one!? Then what?" he asked. "It's both!" everyone (but me) responded. I was puzzled. The research in my eyes had clearly shown it was post. Was I misunderstanding? Misinterpreting? Was there prior knowledge of the subject that I didn't have? What was I missing?


It turns out that the professor agreed - there was so much research supporting the post synaptic cleft, he didn't understand the thought of it being both either. Everyone seemed to note that there was evidence for both pre and post synaptic, and therefore it meant that LTP occurred in both. The professor had made an interesting observation over the time that he'd been teaching the class... That the first years he taught the lesson, the class leaned towards presynaptic. The next few years it was about half and half. A few years after that it was post. And this year it was both.


He ended the class by asking us to wonder about the objectives and interpretive results of scientific experiments. What made us perceive the evidence the way we did? And how was or is that perception influenced by the era in which we study our sciences?

Here's the lesson of the day - I didn't truly realize how comfortable I am in my routine educational environment until I was thrown into a completely new, unfamiliar and complex thread of knowledge... I've never been so attentive when I was confused... And I never thought I would say I loved being confused! I guess that's just another way that this internship has blown my mind. 

Tomorrow our schedule is to go watch Emily's thesis defense in the morning (she's graduating from the program and earning her doctorate!), spend some time working on both of our presentations (for Krista it's Socrates, for me it's next week's introduction and project presentation), meet up with Ashley (researcher from the Salk Institute) and Sabyn (interning at the Salk) for lunch, and finally head off to the Socrates show case! It's going to be a little jam-packed and I'm going to love it.

Here we are, at day five already... These past five days have completely blown my mind - as much as I've learned already, the over-arching lesson I've seen so far is that there are infinite questions to ask and answer! 

Yesterday, Krista and I recorded activity in the morning from the bird we performed surgery on, on Tuesday. It was really exciting to see that procedure come full circle when we attached to lots of cells and were able to wake the bird up at the end of the session. We were able to seal to two cells, which we recorded from. Although we haven't determined anything for sure yet, we're pretty confident that they were auditory cells! 

After recording, we went to a lab meeting in which one of Krista's peers presented his dissertation in order for the group to give him feedback. It was really interesting to watch one of the core pieces of my educational background be brought to my professional future, since High Tech High puts such a crucial emphasis on effective presentation and public speaking skills. Using those skills that I've learned in skill alongside the content that I've learned in the lab, I was able to break-down most of his dissertation and understand it's core meaning. Throughout his presentation, I took notes for myself to remember content ideals as well as what I hope to include in my presentations to the lab. After he was finished, we all headed down to Tim's office to give him feedback and critique. Although I'm not yet knowledgeable enough (my hope is that I soon will be!) to comment on the content as a full participant in the lab, I was able to give advice on the fluidity of his presentation and give him my perspective as a viewer who isn't as familiar with his research as his peers in the lab. It was especially important for me to experience and understand the norms of the lab meeting environment, because next Friday I'm presenting for the lab meeting! So far, I'm a combination of excited and nervous for the prospects of it's execution and outcome, but I figure if I can grapple with the content of the lab, understand the recording process, begin to understand text-based interfaces, and most importantly understand terminal procedures - I can give a presentation on what I know. I'm looking forward to it!

After returning from the presentation, I observed as Krista debugged a procedure in the shaping program. She was using an empty cage box and the stimuli we created in MatLab on Monday to test the procedure of her next project. The structure of these projects take some getting used to (I find myself now near-in-love with them), but I'll give it a shot - The terminal procedure of the project is called same-different (here's one of those intuitive terms I mentioned earlier). A same-different procedure begins a trial by listening to a stimuli. After the first stimuli is played, there is a couple seconds of silence before a second stimuli is played. The task of the same-different procedure requires the bird to identify whether the second stimuli is the same as the first. 

Back to this specific project, Krista is identifying how 'helpful' it is for a bird to have an anchor stimuli when it is discriminating between same or different stimuli, especially when noise (and white noise) is playing in the background. - That's just about the most simple description I can give so far! 

So yesterday, Krista finished "debugging" the program. Here's where I had to make a distinction - debugging is searching through the interface of the program to fix any errors, troubleshooting the program is testing it to see if the debugging process worked and the previous errors have been fixed. Once Krista fixed the final errors, we added spacing between our practice stimuli. Here's something else I just recently understood - The first play of the anchor stimuli is on a continuous stream, we have to manually add in the space between tones. After all the errors were debugged, the next step was to create some white noise in the text program interface of the procedure.

This is when I learned the difference between white noise and noise. Noise (not white noise) is anything that causes us to be distracted from what we actually want to hear. The example Krista gave was being in a crowded room and attempting to talk to one person - we have to filter out the noise that the public around us is making in order to make the distinction between the frequencies of the noises around us and frequency of the voice of the person we want to listen to, in order to hear and understand them. White noise is created through the computer system. There are no frequencies of sound, the values of white noise are random, scattered and purely numerical. The simplest way to make the distinction for me is that noise has a frequency, because there is a frequent wave of sound - but with white noise, nothing is frequent, nothing is related, it's just numbers. It's logical connections like this that I've learned to make at High Tech High, where I have to remember content that seems similar because it's related - you have to come up with tricks for your brain in order to remember and understand it all. 

For today, Thursday (day five), Krista and I are working a little more on developing the presentation for next week and a little later we're heading to a class for her to teach a seminar. More to learn, more to learn! I'm so stoked on everything I've been working on so far and I can't wait for what's to come!

Day Two ... Recording, Shaping and Dissecting! 

I think day two requires a preface of what Krista and I worked on on Friday. Although most of Friday was used to introduce me to everything around the lab, Krista and I were able to go grab a bird (number B767, to be exact!) for me to "shape." (Don't let yourself be confused by the terminology, most of it is pretty intuitive.) "Shaping" basically just means training the bird in a particular behavior that we've designed for it. So after the bird was set up in it's cage, I piled some food on top of the "hopper" for it, so that it would know where it's food will be coming from in the future. The "hoppers" are lift-able food dispensers for the bird - controlled by the pecking of the bird in ports above the hopper bowl itself (unless, of course, the bird isn't shaped yet, which requires you to tape the hopper up so the bird can get food, like Krista and I did for my bird 767 at first).

Fast-forward to Monday, May 27th, which was my second day at the lab. Bird 767 had eaten all the food off the top of the hopper, which meant he knew where his food was coming from, so Krista advised me to start manually shaping him. Manual shaping just means that I stand next to the control board, and watching three phases of the bird's behavior: 1) Standing by or on the hopper, 2) Looking at the pecking ports, 3) Pecking at the ports. When I manually shape him, I have to watch when he does these three activities in order, and lift the hopper by flicking a switch on the control board. This process is designed to first, get him used to the sound, shake and idea of the hopper and second, to get him to understand that he is rewarded with food from the hopper for pecking inside the ports. After Krista and I could see that he understood the process, we started him on a programmed shaping system run by the computer. (If you're curious what a hopper looks like, you can check out the photo on the side bar which shows the hopper bowl and three pecking ports, or you can go the "Photo Essay" page for multiple perspectives.)

Shaping wasn't the only thing Krista and I covered on our second day - we also started recording! The term "recording" is a bit counter-intuitive, because you might assume, as I did, that it refers to recording tones and motifs of birdsong. In fact, recording actually refers to recording activity in a bird's brain. All of this required unique preparations in terms of the system and for the bird as well.

Preparation Krista and I went through in order to perform the recording began with surgery on our bird, which of course was super exciting for me! We started by giving the bird an anesthetic called isoflourane, which is generally administered through a box which is attached to an oxygen tube. In that case, the bird would be put in the box while awake, and removed when it was asleep. Krista, however, being the genius that she is, developed a faster and easier way to administer the isoflourane; she uses the same mask to anesthetize the bird as she does to keep him asleep during the procedure. During that process, she wraps the tip of a latex glove around the end of a small oxygen tube and then positions it around the bird's beak and over it's nostrils.

Once the bird was fully asleep, she attached it to a head plate that clamps around it's beak and through it's ears to hold the bird steady. Then, the surgical process began! The first step was to make sure we could get a clear look at the head of the bird - so we had to de-feather him... Which was actually more difficult that I thought it would be. Once it was de-feathered, Krista used surgical scissors to cut open the skin above the part of the skull that covers the auditory cortex of the brain (the part we care about, and would record from the following day). Once that was done, Krista used dental cement (the goop they use to attached braces to your teeth) to surround the portion of the skull that would be exposed once we shaved off the first layer of skull, as well as to attach the pin which would be used to attach and steady the bird to the recording equipment. Once the cement was laid and the pin was placed, Krista used a Dremel drill to help us reach the trebeculum layer of the skull. The trebeculum is a meshy-looking second layer of skull. For the final step of surgery, we covered the exposed part of the skull with body cast, so that the skin and skull wouldn't heal back or bleed. After we cleaned the surgical area, we brought the bird back to it's home as it started to wake up from the anesthetic. We gave him his food and water bottle back, plus some extra food and crickets in reward of the success of surgery (just like humans, the anesthetic makes the bird a bit nauseous, so his food and water is removed from his cage only for the hour before surgery).