Student-in-a-box

We are almost done studying quantum chemistry for the semester. Up to this point we have studied how to compute the probability of finding a particle in a box or in a well, what energy states are allowed, tunnelling, and such, and we use imaginary numbers for these computations.

We are almost done studying physical chemistry for the semester. Up to this point we have studied phase diagrams, ideal solutions, electrochemistry, among others, and to help us in our derivations we have to assume ideal conditions and/or infinite parameters for convenience.

We are almost done studying biochemistry of the gene for the semester. Up to this point we have studied chromosomal basis of inheritance, the central dogma (replication, transcription, translation), reverse transcription in viruses, epigenetics, and regulation of gene expression, to name a few. We learned that we needed powerful microscopes and supercomputers to see and analyze our DNA, and protein structure modelling is necessary to visualize how our proteins and enzymes are built, and how their active sites interact with substrates.

We use imaginary numbers, and we make a lot of assumptions at the infinite scale. We rely on simulations, and an understanding of how molecules and ions behave with itself along with other molecules and ions to study things we cannot see but are very much observable in everyday life.

We are almost done with the semester (or the semester is almost done with us). For a while we have been sitting in front of our laptops all day, sometimes unsure of why we have to derive the angular momentum operator or determine the eutectic and peritectic points on a phase diagram or why we are in a simulation website dragging an icon of a P200 micropipette into an icon of a tip box to attach a micropipette tip. We are uncertain on what to make of all of these once the semester ends, once the supposed internship begins, once thesis season begins, once we graduate, after we graduate…

We can have simulations in our head of what will happen, we can have imaginary scenarios and infinite assumptions, infinite worries even, because we cannot really see what kind of future is in store for us, much like how we cannot see electrons with our naked eyes. However, unlike in the lessons we discuss in class, the imaginary things, the assumptions, and the simulations we have do not modify our problems in a way that is more convenient for us to solve.

Quantum mechanics becomes classical mechanics as an object of interest increases with size. We cannot explain why electrons can pass through boundaries and have discrete energy levels if we do it classically, while with the quantum approach, we cannot explain why Earth’s location and momentum can be specified simultaneously. Somehow, in these surreal times, we have been embodying this uncertainty principle: unsure of where we are when we know (or we think we know) where we are supposed to go, unsure of where we are headed to when we know where we are. We are in an infinite loop of doing requirements while attending zoom meetings for the sake of submission, of waking up to do assignments because there is a deadline while we do not know if we are learning or not. What is all this for?

In DNA mutations, we have what we call a point mutation wherein a single nucleotide changes. If transcription into an mRNA yields the same amino acid, it is called a silent mutation; if different amino acid, missense mutation; and if stop codon, nonsense mutation. A point mutation may not affect us at all since more than one codon can encode for the same amino acid (very clever), but a point mutation may also cause something as severe as sickle-cell anemia. Just one mistake does that. One mistake probably brought us to what we are experiencing at the moment, one mistake which led to another mistake and another and another… Or maybe the lack of urgent action domino-ed its way to where we are, much like how deletion of n nucleotides causes a frameshift mutation which affects the amino acid chain, and thus the structure and function of the protein. We are getting older, and there is not much room for mistakes, but then here we are, placed in a condition where there is even less air to breathe, quite literally.

Unlike scientific theories which make good estimations of natural phenomena, unlike in derivation where we know which are constant and which are variable parameters, unlike in integration where we can have definite bounds, unlike in the laboratory where we can set optimal conditions, we are very much in doubt of how long our situation lasts, what happens after our situation if our situation will be over at all, and if there are still chances left for us. However, I do hope that this situation is just one bad semester which seems to be stretching and compressing time on its own, and, like a black hole, is sucking our energies, but will at least be over. I do hope that this situation is just one bad essay that needs to be finished soon, or better yet, now.