What a short three weeks it has been - what an incredible experience! I have never felt so privileged to be a participate in academia as I have these past weeks. It's unbelievable that I've been able to accomplish so much - and I have Krista to thank for all of it. She's been a truly amazing mentor, answering my questions not only in detail but also in a context which made it both understandable and applicable to me, aiding me in completing various new tasks, and teaching me how to participate in the vast world of science. I feel like the luckiest intern in the world, especially knowing that I get to continue working with her in the lab this summer. (Thanks, Krista!)


It'd be easy for me to say I've always known I've loved science - but I think that'd be a lie. I went through phases of wanting to be a rock star, a dancer, a photographer, a visual artist, and then I didn't really know what I wanted to be. There were little steps along the way that lead me to the path of science and medicine, but those careers seemed so untouchable to me that I didn't really even entertain the thought of them. 

When I was around the age of seven, I was at the Discovery Store with my mom (who is a teacher, and a lover of all things related to unique and interesting children's activities). We stumbled upon an anatomical doll - one that was clear, cut in half, and filled with removable muscles, bones and organs. I fell in love with it, as any seven-year-old would, right? Of course, we took it home and within a few days, I'd already taken apart the doll and put it back together a few times, before I even realized there was an instruction manual with pictures of how the doll was to be put together. That's kind of where the subconscious love of science began... which lead to my first-ever heart dissection of a Thanksgiving turkey in third grade. I didn't think it was weird until my friends were grossed out by the fact that I liked cutting up organs. I guess it's still a bit strange. What I'm getting at is that my brain was kind of made for taking things apart, absorbing them, and putting them back together. If you've ever had a class with me, you know that I love asking questions, especially ones no one can answer, because that means I can compile the answer myself... but I never really connected these 'traits' to a career in science; I'm not really sure when that connection was made. Probably when I figured out that I wasn't the only weird one in the world who liked to look at organs, take things apart and put them back together. There's actually a name for people in that profession - they're called surgeons. 

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How has this experience made you consider your college path that will ultimately lead to your career?
Being at the lab has really opened my eyes to the range of options that lay ahead of me, and it's made me realize that there's not really one single path for scientists. There were so many levels of the internship that helped me find my feet in terms of my future in college. The most basic thing I learned was that I don't have to be one hundred percent perfect at everything, although it is important to be well-rounded. Science is collaborative and the environment entails that there will be people who are educated, talented and most knowledgable in necessary areas in order to find solutions, and all those people will work together towards a common goal of achieving such a solution. In terms of college specifically, I guess I fell in love with the UCSD campus just a little bit. I appreciated the overall structure of the school, Muir college especially. I can definitely see myself being successful there, and thanks to the participants in the lab (Krista, Tim, Jordan, Emily, Dan, Justin) I can see myself being successful in science, labs, research facilities, medicine and beyond.

Consider what you have observed and learned about your mentor or other employees at your site, and reflect on your own academic & professional preparation.
The lab members are all well-rounded; they have various interests which included specific focuses. Krista, for example, is especially interested in Neuroscience, but members of the lab are also focused on behavior, psychology, and neuro as well. Krista and I spent a lot of time talking about my options when it comes to college choices. She mentioned that smaller schools often offer more (and occasionally better) opportunities for under graduates to participate in (and even conduct their own) research. I also learned about an MD/PhD graduate program in the UC system which sounds absolutely perfect for me. What I found overall is that, as I said, I really have endless options. I just need to decide what's best for myself, with considerations to my strengths and areas which I hope to grow (including traveling!).

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How was your work as an intern meaningful to your education?
Conceptually, I have grown immensely from this internship. I've gained a deep understanding of content which I had already learned, and I have seen it be applied in a setting which is highly applicable to my future. If I've learned anything from my internship, it's that everything in the world is extremely complex, nothing is really ever 'simple.' What seemed so simple to me was allowing myself to really enjoy the experience and be excited about the little finite details - because there are SO many of them! One of the big over-arching lessons I've accrued through the internship was the contrast between the presentations which we do at High Tech and the presentations in a lab setting. In my previous experience, the intent of a presentation is to exemplify one's knowledge in detail of a subject, and possibly to teach that knowledge to a greater audience. At the lab, the purpose of my presentation was purely to introduce the major ideas of our project to the lab, and complete knowledge was not required because the presentation was collaborative with everyone in the room. The format and content of the presentation I gave last week was completely new to me, and it was therefore the most difficult presentation I've ever given. So much of my internship was meaningful, that it's been a challenge to condense the relevance of it in a way that is simple to share with the world.

How did your project go from an idea or inspiration to a final product?
Krista and I used inspiration from current and past projects at the lab to design our project. It was a bit of a compilation, really. A recent focus of the lab is on the cocktail party problem, and the design of our specific task of a perceptual anchor and noise offered me a lot of opportunities for exposure to procedures. Reading about the perceptual anchor phenomena not only allowed me to be exposed to terminal procedure, but also helped me to understand the theme of the lab, the roots of our research, and it was my first exposure to published scientific papers. The topic of auditory perceptual anchors also connected to recent research on dyslexic humans, which aided in my understanding of the relevancy of our project, and helped me to develop an idea for my senior project. Through our project I've also been able to use new programming equipment to create figures of data, formulate tone stimuli using purely text-based interface and mathematics, and in the future I will use the same program to create motif stimuli for our birds. This project offered so much potential for growth - we started by figuring out what we wanted to work on, what I needed to learn, and developed a project that allowed Krista and I to explore different subject matter in the lab.

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What new appreciations did you develop while working as an intern? Why?
I have such an appreciation for the finite details of the world. Who knew things were so complex? I guess now I truly appreciate the idea that we will never really understand everything in the world, or the universe for that matter. There's always more to know - and that in and of itself is absolutely astounding. 

What qualities or characteristics did you see in the people around you that you want to develop in yourself? Why?
Everyone in the lab is one hundred percent dedicated to the work they're doing, but they don't let their drive for success get in the way of their personal health and happiness. So many of the lab members are physically and socially active - you have to be when you spend almost all of your days working in front of a computer in a basement with birds for company! I think both the individual work and the need for collaboration really contribute to the familial connection in the lab, but I can tell you for sure that there's no greater group of people than those in the Gentner Lab. Each of them contributes strong and meaningful ideas with confidence, and they support the ideas of others with grace. They are all admirable individuals.

Today we started off by doing some slides of the brain from B724, which we recorded with last week. I've found it really exciting to become more independent with the histology work... although I am still a little fearful of the oxygen tube required to make dry ice (so that we can freeze the brain to the slicing stage and prevent it from wiggling around while we slice... not that it can wiggle on it's own... you get the point), so Krista still makes the dry ice for me, but other than that, I fly pretty solo when it comes to slicing and histology!

← Brain on the slicing stage!

Today we got our first slices in which we could really visualize the fluorescent dye. We apply the dye to the end of the electrode probe we use for recording so that when we're finished recording, and we work through some histology, we can see where it was that we did (or didn't) see a lot of activity in the brain. The region we're focusing on is auditory, and it's scientific name is "Caudal Mesopallium" or "CM." 

We found with the slides from B724 that we most likely did reach CM, which is great news, since we got a lot of activity while recording. 

For each hemisphere of the brain, we can create three slides with eight 100 micron slices, for a total of 24 slices. Based on what I saw today, I'd say that a little less than one third of the slices showed evidence of dye (evidence of dye = evidence of penetration in that region of the brain with the electrode while recording). We use the fluorescence when we review the stats and results from recording... which I have yet to do, but I'm pretty sure it'll be exciting since there was so much activity during recording! (Besides, everything I've seen in the lab has been exciting for me!)

In order to visualize the slides with the microscope after mounting the slices of brain onto their slides (in order, in 100 micron slices) we photograph the slides without the fluorescent lighting from a mercury bulb, then with the fluorescent lighting. With some of the slides, we can really see the dye without the aid of fluorescence - but we check all three slides from each hemisphere for fluorescence just in case. 

We've (mostly Krista has been) debugging our behavior program today as well. It's been really rewarding to see all the preparation come to a circle (I'm not ready to say full circle yet - I'm not ready for it to be over!). Today the pair of us acted as subjects to our trials, responding correctly and incorrectly in order to test the program. We found a few "bugs" (such as the lack of a recording of data when the subject responds incorrectly)... I think I hear Krista running the program right now! I was a little proud of myself today - After watching Krista run the program for two weeks (man, time flies fast...) I finally killed and started the program before and after she debugged! (The score between the program and I is "Sophie: 1, Program: I've lost count...")

Hopefully my excitement is showing through, I've been having the time of my life in the lab! I feel insanely lucky to have such an incredible mentor - she's allowed me to really approach this internship full-force and get the best learning experience possible from these three weeks. I can't wait to continue working with her (and the rest of the lab) throughout the summer!

I'd best not get ahead of myself, we still have one week left (two presentations to go!) and the day's not over yet!
Krista's been recording from another bird and we're planning to nissel stain the tissue slices from this morning sometime this week as well! Busy times as always, but the work never fails to seem like fantasy and fun...

We're studying the phenomena of perceptual anchors - modeling our questions with birds and applying our answers to humans...

In the most simple terms - this is our project; to create an experiment that can apply the Cocktail Party Problem to birds in two different contexts. But first! What is the cocktail party problem? (In my understanding, the best way to explain it is by example and I'll try to be a little creative with mine....)
Have you ever been driving in a car with the windows down, music blasting, and the person you're driving with suddenly wants to spark a conversation? You don't want to lost the wind in your hair, nor miss your favorite part of the song, but you still want to try and engage in conversation with this person, right? When you're trying to listen, pick out and determine what the person is saying, your brain is doing the same thing - trying to detect, recognize and discriminate what that person is saying from the music and the wind. - This is the basis of the cocktail party problem: having to separate all the 'noise' around you from the sound (or in this case the voice) that you actually care about. The name "Cocktail Party Problem" comes from being as a busy party, where there's voices, music, and various other background noise preventing you from clearly hearing the single individual you're conversing with. 

What we've learned from Dr Dan Meliza's paper, "Effects of auditory recognition learning on the perception of vocal features in European starlings," is that european starlings definitely benefit from having experience with an anchor stimulus, when they have to discriminate between multiple tones or motifs... Therefore, Krista and I are going off the work of that study to ask about the variability of that anchor stimulus when it and a target stimulus (second stimulus played, which the birds must classify as 'same' or 'different' from the anchor) are embedded in noise....

Why is this research relevant to humans? You might ask Dr Merav Ahissar, who wrote a paper on the audio anchoring ability of human beings with dyslexia, called "Dyslexia and the anchoring-deficit hypothesis." Dr Ahissar's paper provides data that dyslexic individuals lack the benefit that having an anchoring audio experience provides. There is a distinct connection between the 'anchoring-deficit hypothesis' and the ability of birds to benefit from anchor experience when their audio stimuli is embedded in noise.


Here's where Krista and I are at in our experiment:

1. Four Blocks of Shaping - In order to train them to adapt to the hopper system and respond to both visual and auditory stimuli given to them. 
2. Same vs Different Trials - These were the first set of discrimination trials we gave to the birds, requiring three steps: a) peck center port to initiate a trial, b) peck center port to acknowledge participation in trial once the anchor stimulus has played and to begin play of target stimulus, and c) peck center if target is the same as the anchor / peck left is the target is different from the anchor... This process was not effective for the first round; we found that the birds only repeatedly pecked the center with no regard for their punishment when the target was different from the anchor (meaning that they should have pecked left).
3. Different-Only Trials - After the birds were unsuccessful in round one their same/different task, we decided we had two options, to either: increase the length of their 'time-out' punishment time, or put the birds on different-only trials. We chose the latter. The birds all ended this round of the trial successfully, though at different levels. 
4. Increased Anchor Play (via Variable Ratio) - In order to give the birds more of a challenge, we attempted to give them a change in the number of times that their anchor stimulus would play. This was unsuccessful however, because the birds were relying on the pattern of the task rather than the stimuli in order to respond.
5. Visual and Auditory Stimuli - Now we have the birds on a trial in which they are provided with visual stimuli queuing them in the port which they need to peck. The idea of this intermediate terminal procedure is to get them relying on the stimuli when they respond in a trial. Over time, we'll wean the birds off of the visual lights in the port they need to peck, once we're assured that they understand the trial stimuli-response protocol.

His·tol·o·gy (noun) /hiˈstäləjē/
The study of the microscopic structure of tissues.


Today was a short day - but no time is ever wasted in the lab! Krista spent some time recording with the bird we gave a skull cap last week during surgery, and she got me started with doing some histology - or in more scientifically romantic terms - brain slicing!

Since today was my first day working with histology, Krista gave me some brains she'd saved but won't be using in the future for testing or anything - the perfect first-try specimen! Of course, as with every scientific procedure, there were many steps I quickly learned for the process of setting up the materials. 

The first step, of course, is slicing, so we have to make sure we have all the correct materials in order to start. Krista set out a petri dish, a scalpel, a multiple-welled dish, paint brush, some sucrose solution, phosphate buffer, and of course, the brains! Basically the first step is to freeze the brain to the holding plate, using sucrose (sugar) and dry ice. From there, the plate moves 100 micrometers by itself every time you retract the blade of the slicer. 


It takes a few tries to get a solid slice - one without any tears, or bits of brain missing - but when you do, the brain unfolds beautifully once you drop it in a well of PBS (phosphate buffer solution). Krista told me, and I totally agree, that everyone has a unique technique for slicing that works for them - and man, if anyone ever questioned whether science and art were related, they must have never done histology... or sliced brains... or dissected animals parts.... I dunno, I guess for me the most simple definition of art is whatever makes you feel something. Whether it's melancholic, or passionate, or blissful; whatever that thing is that makes you feel that way - do it. That's your art. I guess for me it's science; and doing all the work at the lab has made me realize that. I mean, sure I've always loved to learn, and I love doing the work at school because it makes me proud, but it's things like listening to great music, or dancing, or dissecting hearts or brains or just organs in general, or even learning the answers to endless questions, that's my art... and it helps to see a little bit that brain slicing involves the use of a paintbrush. 

Have you 'Matlabbed'?
Okay, so maybe "Matlab" isn't a verb... but it definitely should be. It's basically the universal program used to design terminal procedures in scientific research labs, and today, I can proudly say that yes, I have 'Matlabbed.'

Just to give you a plainly basic understanding of what Matlab is... there is no basic understanding of Matlab. Especially to someone like me who's never used a text-based interface before. In all seriousness however, Matlab is basically the tool used to design, analyze, edit, debug, etc the entire program of a terminal procedure.

Aside from Matlab, Krista and I got a lot else done today too. We started off the day by doing surgery on one of Jordan's (another grad student of the Gentner Lab) birds he had finished working with. We followed the same procedure we did the first time we performed surgery (which, of course, was equally as exciting for me).

With this bird, because it's already been trained and recorded for research, we're using Urethane to anesthetize him during our recording procedure (this time I got to administer it to the chest muscle of the bird!). Previously, we had been using Ketamine, which allows him to wake up from the procedure. Urethane, however, has protocol that requires us to euthanize the bird post-recording. This allows us to record for any length of time. However, because today he was used to record from around 12:00pm to 5:00pm, he's been waking up a bit because his internal clock is activating his muscles (starlings usually are most active at night).

We (Krista, as I occasionally observed) were able to catch a few cells today. Krista suggested that we administer sucrose (sugar; any chemical ending with "ose" contains sugar) throughout the procedure so that the brain would receive fuel from food. We won't be sure until we check out our data whether this helped or hurt our results.


While the recording was going on, I cleaned the bird's cages, which simply requires me to change the cage paper, administer food in less-than-full hoppers or food bowls, refill water bottles, clean empty cages. I can gladly share that I have become adjusted to the potency of the smell in the cage room to the point where I can no longer smell anything in there at all. :)


Today was also a big day for another reason - the start of trialing all three of our birds in their terminal procedure! We started two of them off by identifying tones as the same or different. A tone is a single frequency, basically like a note; in this case, our tone was created in Matlab, so it sounds rather robotic when compared to the tones of the starlings.

We found that in this first round of procedure, the birds were infrequently being punished and rewarded, because instead of waiting to respond to the trials, they were just incessantly pecking the center port of the hopper. Before we get into details of trial analysis, let's cover the basics of our terminal procedure.

First, the bird initiates a trial by pecking the center port. The computer then plays the bird and anchor stimulus, which is the tone they use to determine whether the second tone is the same or different from. The second tone played is called the target stimulus, because we want the bird to respond to it. The bird pecks the center port if the target is the same as the anchor, and the left port if the target stimulus is different (the right port, at this point in the project, is not included in the responses; we also record when the bird initiates a trial but doesn't respond to the target stimulus). If the bird responds incorrectly, it is punished by having his light turned off for a few seconds. If the bird doesn't respond to the target stimulus, nothing happens.

Back to results from the first round - all three birds were found to be pecking repeatedly at the center port, rather than taking time to analyze the stimuli and respond with either the center (same) port or the left (different) port. To solve this problem, we added a second layer to our procedure, called an intermediate procedure. We designed our intermediate procedure to be all different trials, in order to teach the birds to peck the left port.

At first, the birds displayed the same behavior in relationship to pecking the left port as they had previously with the center; they figured out that they needed to peck the center port to initiate the trial, and that the left port would get them food. The caveat to this habit is that they would be punished for responding to the stimuli too early (ie, before the target played or before it was finished playing). 

We then found with bird 1153 that it's behavior changed when it understood it's punishment. As shown by the left chart, the bird's percentage of accurate responses increased with every trial... and by the end of the night he was approaching 100% accuracy!

The x axis represents block number (or group of trial responses by 50's; there are no half-integer block numbers, Matlab adds them automatically), the y axis represents percentage of accurate responses (in percent of 100).