and so it goes

Today I decided to drop my biology seminar in favor of keeping all of my chemistry courses. I'm feeling good about this decision, and I have a tough semester ahead of me but I really like all my courses (well, besides stat therm, but stat therm is a necessary evil), and regardless of whether or not it's more or less work than my other classes, it is one more thing to keep track of. The course is offered every year so I can take it next year, and bio seminars are good courses to take as a senior. I haven't attended it yet, which makes it easier to drop, and I really like my advanced mechanistic organic chemistry class. Advanced mech only has 5 people in it which gives it a nice small feel, and overall it's just a fun course. Which means I'm taking all chemistry courses, and only 3 units (technically). Inorganic (even without the lab) and stat therm in particular are highly time consuming courses and not going to seminar on Wednesday nights gives me more time to hammer through psets and study for them. I have a good feeling about this semester; not taking any biology courses is going to be a little weird, but whatevs, at least I have biochem.

It also gives me more time to play with my little project (although PEOPLE KEEP USING THE COMPUTER LAB SO I CAN'T USE SCI-FINDER! grrrr).

Onto making flashcards to help me memorize the periodic table for inorganic.

I feel like my rather shitty math background has been a constant handicap. Due to the fact that the math department at Reed only teaches theoretical math geared towards math majors, and due to the fact that Rao (the math head) determined my semester of calc I at UIC as equivalent to Reed math 111 (calculus), I have managed to skate through Reed college only taking probability & statistics. Because of this wacky math system, math 112 is more introduction to proof writing than a calc II course, and I was told that unless I was really into theoretical math it wasn't going to be fun and it certainly wasn't going to be useful. I never took calculus in high school and I didn't want to push physics to my junior year (thank god I didn't).

Due to this situation the chemistry and (especially) the physics department pick up some of the slack. Yesterday I learned how to take a second partial derivative with respect to two different variables. Having never taken a multi class, I picked up the concept of a partial derivative and how to do it in intro physics when learning about the wave equation. I had never seen the notation for a double partial derivative before. I'm a little shake on integral tricks too.

I'm usually ok with this fact, and I've kind of accepted that I'm more prone to think about the world in descriptive terms. This doesn't mean that I'm not down for a few computations, but I'd rather plug it into a modelling program or mathematica. I'm good with scooting around arrows, stability rationalizations in the style that organic chemists do it, and basically things that operate in pictures and words with small amounts of algebra and maybe a derivative or two. I love to learn about biophysics and I think the techniques that are out there are quite fantastic, but my understanding of them is all in pictures and words. Same goes with NMR. My feeling for the physical world is one where math is a tool, but I'm not interpreting it through it. I see math is a way to get better pictures in my head. This is at a stark contrast to the way physicists--and for that matter, even physical chemists--seem to view it--as if they interpret physical phenomena through math.

I'm re-learning about the quantum numbers for inorganic (I learned it in intro chem once but forgot) and there's always something in the book like "you can solve the Schrodinger equation for hydrogen and hydrogen-like nuclei, but we're not going to go into it in here" and sometimes it makes me feel bad about not taking quantum. It's like, even though I did quite well in my synth class, I feel like I don't have quite the feeling for what is all behind it as some people. I know that what I learned in intro physics I generally rarely use beyond bits and pieces here and there, but it was good for backing up my general physical intuition and understanding for how things work. Conservation of energy, waves, momentum, acceleration, electric and magnetic fields, these are all fundamental things that I need to understand as any sort of scientist--and are even helpful conceptually for biology. Ploughing through it all, I can't really do those problems anymore but I left with a better conceptual understanding of the physical world. Dan reminded me the other day that physical chemistry does this for other types of chemistry, i.e. the pictorial representations of stability rationalizations are quantifiable (well, sometimes) and that's where the theoretical basis for these qualitative observations come from even if we don't always have the computational power and models to find them quantitatively. It doesn't mean I have to want to be a physical chemist, but I do realize the power in other chemical approaches and understand why I need to learn about them.

I think a lot of my issue with math is a lack of confidence from being "bad" at it for so long. I mean, calculus is a tool like algebra and not like WHOA COMPLICATED OMG MAGIC!

On the up side, speaking of nice, fuzzy picture-based synthetic organic chemistry, Pat gave me a little project to mess around in the lab with. He gave me a couple compounds he'd like to make and test the pKas. I need to go play with Sci-Finder to see if they have been made before. This is good; they're small molecules and models for the types of compounds the lab as a whole works with, but in the past the research I did with him was more guided like "here's this idea I got, I'd like you to try it out" instead of asking me to find preps that I might be able to run. I also know more chemistry and know how to use Sci-Finder better than I did when I worked for him last summer, though.

This Upcoming Semester

I'm enjoying these last few days of basking in winter break (classes start up again on Monday); browsing the Internet endlessly and guilelessly, watching TV on my computer, and drinking with my friends. But I'm gearing up for the start of a new semester that will hopefully be good.

Between my theoretical organic chem class (advanced mechanistic organic chemistry) and my intro inorganic class, I'm hoping that MO theory might actually make some semblance of sense. A professor described it once as "chemistry's version of the stork story", so I'm aware of some level of fundamental bullshit going on in describing orbitals and chemical bonding, but I'd really like it to be a little more coherent in my head conceptually than it currently is. When I tutor organic chemistry sometimes I feel like a total faker, drawing meaningless balloons and calling them a HOMO and a LUMO. I understand it well enough to sort of describe what's going on in the Diels-Alder, but just barely. I've been introduced to some ideas that are useful mnemonics for stereochemistry and useful to know to generally understand what's going on in the lit in synthetic organic chemistry (concerted reactions, thermally allowed vs. photochemically allowed, chair like transition states, etc.). But apparently this class goes really into the Woodward-Hoffman rules, and I imagine that conrotatory and disrotatory will mean a whole lot more to me after the end of the semester than it does now. I'll also get a better grip on how to use Spartan, which will be good because computer modelling is useful and not something I am terribly comfortable with.

I'm hoping that i-chem will fill some gaps I currently have in my chemistry knowledge. I felt both in synth and in biochem that some things would have made more sense having more background in inorganic. In any case, the textbook looks pretty interesting and it's a chance to do some totally new chemistry. Along getting a better grip on MO theory, I'd also like to get a better grip on coordination chemistry and remember that d orbitals actually do exist. And to be reminded that there are chemists who don't view carbon as the center of everything and who regularly look beyond the first two rows of the periodic table.

Statistical thermodynamics, my physical chemistry course, looks pretty gross. I know I shouldn't be closed-minded, but I was flipping through my book and saw the return of angular momentum and it gave me chills flashing back to intro physics. I know I'll get through it and I know I'll appreciate it in retrospect, but...it'll be a slogging through it experience. It's going to be a lot of math--and I'm much more into the descriptive aspects of chemistry, or at least that part comes a lot more intuitively.

It's going to be a very chemistry-intensive semester; I'm only taking one biology course and it's a seminar on membrane-membrane interactions that meets twice weekly run more like a journal club than a class, not a full lecture-lab course. This is the first time I've taken so much chemistry at once and I hopefully won't OD on it. It's also pushing me out of my chemical comfort zone of pushing around arrows, but that's probably a good thing.

I'm also excited about my independent study. It's a not-on-the record, not-for-credit thing, which is good because it means I can do as much or as little on it as I have time for. I'm not sure exactly what my synthetic target is going to be, but I've worked in that lab before and the research done in there is ongoing, so I'm familiar with the overall project. I'm going to chat about it with Pat (the prof whose lab I'm working in) on Tuesday to work out some details. I'm not sure if I'm going to continue to TA organic lab this semester or not. I was asked for my availability, but I think it depends on how people's schedules work out. I'm also only taking one lab class--biochemical methods--which is the first time this has ever happened in college. In the past I've always taken two or three labs at once.

I have to take my quals this upcoming spring. Reed sort of mimics the PhD system and junior year you have to take junior qualifying exams in your major before you can register for your senior thesis. As an interdisciplinary major, I need to take both the biology exam and the chemistry exam, so that's going to be two intense weekends this spring.

And then...wow. Next year I'm going to be a senior. Next year I need to take analytical chemistry, one more liberal arts course to fill a group requirement, and my thesis and then I'm allowed to graduate. Crazy times.

Trials and Tribulations of undergrad projects

So at Reed we do independent projects in biology classes. They're usually kind of fun, and it's kind of a unique part of the curriculum here. However they get annoying for the following reasons:

1) we have 6 weeks to do them, so we are discouraged from doing time consuming or complicated techniques (because you just can't)
2) We aren't allowed to do something expensive. If we need to buy something expensive (like, say, a $300 antibody), we better damn have a reason for purchasing it, like someone else in the department will use it later. It can't just be your pet antibody for your pet protein. We used to have the resources to write a grant for expensive materials for independent projects, but one of our big teaching grants has run its course, so the department is tighter on cash than it has been for a while.

This makes sense; we're a small liberal arts school with limited resources. Our science program is solid, but as a small liberal arts school we don't have a lot of fancy schmancy equipment nor do we have a large budget. The opportunity to do independent projects is great for gaining lab experience, and a great opportunity, but at the same time, more of the money is spent on the faculty's research and people's undergrad theses. As it should be.

Depending on the class there is more or less guidance. Animal Physiology, Bio 381, happens to be a junior/senior class. Thus, there is little guidance at all and we are encouraged to think like scientists and figure out our own problems based on issues we are interested in. Good, great, I'm liking that. But it's hard because...shit son, it's hard enough to find an experiment that hasn't been done before, period. Add that on to a no more than 30 dollar budget and a 4-6 week time scale, and you have really slim pickings.

So we searched and searched and found this interesting pro-apoptotic signalling molecule, ceramide. It's kind of neat because it's a structural membrane lipid as well as being a pro-apoptotic signalling molecule, which is unusual. An experiment in the past showed elevated amounts of ceramide in the prescence of ionizing radiation (well in this case gamma radiation), in similar fashion to the way it was elevated in the prescence of TNF alpha (tumor necrosis factor) and chemotherapeutic drugs. Well, Reed has a nuclear reactor, kind of one of those odd little anomolous things--I'm actually a licensed operator, it's nearly completely run by undergrads--so it seemed like a good resource to take advantage of. Why not repeat the experiment looking for ceramide levels, but look for it with a greater variety of types of ionizing radiation (neutrons, gammas, and betas) in the reactor? Well cool.

Except then the issue of how to quantify the ceramide comes up. There's a kit that uses a radioactive phosphorous and a kinase, but that kit is expensive. No dice. Using a HPLC is probably the easiest method, but to my knowledge, both the HPLC in Arch's phyisology lab and the HPLC in the organic/biochem reasearch labs are not up and running. Okay. Oh here's a method, you can 1) extract the lipids out of the cells 2) run some silica gel chromotography (we found an elution plan in the lit) 3) functionalize it with benzyl chloride 4) do absorbance studies. Oh wait, forget that silica gel chromotography is a pain in the butt, that would take a shit ton of cells, we'd need to check to see if we actually purified it with the GC-MS/NMR, and...well....that's not exactly happening in 6 weeks on top of coursework. Okay, nix that.

Well, it turns out that a molecule in that pathway, spingomyelin (well, it's actually made from spingosine, but it's in the same pathway) turns into ceramide. So it would just be easier to take a look at upregulation or downregulation of the spingomylenase. We found a paper (which I don't have on hand and am too lazy to look up) about how TNF alpha and chemotherapeutic drugs lead to an upregulation of singomylenase, just as they lead to elevated levels of ceramide. BUT, no experiment was done with ionizing radiation. So, bingo. Primers are cheap. These are even published, so we don't have to worry about our primers not working (even if primer 3 input has done me well in life for designing primers for arbitrary genes, it's always nice to be assured that they have worked in the past).

Okay, problem. We asked if we could culture some fibroblasts to do the experiment. And got a "no, it's too complicated to do in 6 weeks". But I mean, if we take arbitrary dead tissue, that's confounding the experiment. Ischemia causes apoptosis and we're studying apoptosis! Not cool. I mean I see what he's saying, but damn. He suggested looking into using, say, sheep's blood. That shit is cheap. He also said using qPCR was unnecessary. Well, everyone uses qPCR now. Band brightness is a shitty way of determining upregulation vs. downregulation. I mean, I know that the qPCR machine is in heavy use by people doing their theses and the cytogreen dye is expensive, but it's really hard to make any sort of real interpretation of anything by band brightness and no one really does it anymore.

So here we are. We tried to come up with a cheap, fisable experiment and got shut down. All due to culturing a few fibroblasts. Maybe we can still do this experiment with sheep's blood? Or maybe the cell bio prof has a few extra cell lines floating around her incubators?

In a similar fashion, anyone who wants to do a Western Blot pretty much, well, can't unless they are studying a protein that other people in the department are studying.

This shit is hard.