It was such a joy to read your letter Tugba,
I realized a mistake I often make when I get frustrated when the right action, which is often the most obvious, is not taken. I assume that the person can also see what I am seeing because, well, it’s right in front of their nose. But dear, the authors were right. Just because something is there somewhere where we look at it every day doesn’t mean that we “see”, “understand” or “comprehend” it.
Coming from a similar background, I know your pain. The first time I realized something was lacking in our education system was the first year we moved to Istanbul. As a transfer student from Hatay, I knew more about certain subjects in English than my peers in Istanbul. I had to witness a teacher blaming an entire class for failing an exam because they didn’t know what a question tag is. A concept that has never been introduced by that teacher. How come Ozge knew about it if she had never taught it? She didn’t even find it odd that only a single person could answer that question, let alone consider the fact that I was a transfer student.
Could students have learned it on their own? Perhaps. But all we knew at that grade was to study for exams. You live, breathe, and die for exams to get you into the best school and the only method we are told to apply is memorization. This memorization has hurt me in biology quite a bit. Consider the binding of a ligand to its target. Teachings are often structured to tell you that ligand A, binds to target X and Y and doesn’t bind to Z and this is the binding site in X and Y. The importance of concentration, whether the target is tethered, how diffusion plays a role, or how on earth ligand A finds that site on targets X and Y is often ignored. I understand that we still don’t know everything about these processes but why it was never posed as a thought-provoking question when we first learned about “binding” at the university? It should be important to let the mind, which has just heard a new concept, explore the facts and unknowns. If I had questioned these concepts back then, perhaps it wouldn’t come as a surprise now when I see wildly different outcomes from different types of binding experiments.
There were moments that I remember fondly though. One of them was when I realized how much I was lacking in the questioning department. In an exam, we were asked if elephants get cancer, and why. Up until that moment, I had not even questioned which beings would get cancer, elephants weren’t model organisms, I had not seen one in real life, and we didn’t have them in Turkey. So they were not at the top of my list so it was ok that I didn’t know the answer. But why I had not asked that question about other animals around me? Did I know if dogs get cancer? What about birds or insects? I probably wrote a nonsensical answer to that question but it got me thinking and sometimes I think exams should be just about that.
I have actually learned my lesson and I am self-correcting. 1.5 decades later I found myself questioning whether trees get cancer while staring at a tree with some strange growths on it. I suppose my point is, I agree with you. Memorization is a tool that we use without much knowledge of the tool itself. Remind me to find that website for learning quantum computing. They were applying a method where you would be sent short questions about what you have read at short and long time intervals. I really liked it, although, for some other reasons, I haven’t progressed much in my reading on quantum computing. You could give a test yourself and see if it is effective.
I wrote and rewrote to write a concise letter yet it still came out to be a long one but I hope you’ll enjoy this brief touch on my learning experience. I have been busy finding some odd examples in the RCSB database. When this database was first introduced in the classroom, I don’t think a big emphasis was placed on the “biological assembly”. The examples showed that you could download the “asymmetric unit” file and you are good to go. But this one particular example I came across is a good teaching example and demonstrates how important it is to use the biological assembly file.
I first read the study of He et al (DOI: 10.1126/science.1062246) and was taken aback when the authors mentioned how different the structure van den Akker et al had published was from what they obtained in their study. I was looking at the said structures and they were similar. What was going on here? Following the van den Akker et al (DOI: 10.1038/35017602) article and looking at the entire deposited entry I realized the articles were published based on the asymmetric unit and I was looking at a biological assembly. Perhaps the entry was modified to reflect the newly obtained evidence. But articles being a frozen entity in time couldn’t reflect that. You can also see how there was a discussion between the two first authors. Don’t you love when science is all about moving forward, rather than being right all the time?
My surprises and frustrations with PDB files never end. Do you get frustrated at the PDB files as I do? Programs’ own way of handling PDB files in the way it pleases them is another bottomless well of frustration for me. What are you up to these days? I had seen your photos at the annual biophysical society meeting, you looked so happy after the session. I am glad that it came out as helpful as you imagined it to be. I am curious to hear more about the thought process that you had when organizing the event. What would you keep the same, and what would you do differently for the next year’s Biophysics 101?
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