There's so much to chemistry

Basically what this semester seems to be boiling down to is physical and inorganic chemistry are waaaaayyyy different from organic. Jesus christ.

I've been fussing around trying to calculate the numerical radii for the radial nodes of a 3s and 3p orbital for frickin' ever.

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.

First day back

As predicted, my chemistry courses are pushing me out of my comfort zone. Inorganic and stat therm are totally different types of chemistry from what I'm used to dealing with. Even adv. mech is pushing me out of my comfort zone with some tough Diels-Alder structures. I'm ok at seeing them retrosynthetically (I think probably from reading Totally Synthetic)--but for some reason the product picking and remembering the endo rule is harder for me to put together since I don't have much experience with dealing with pericyclic reactions. I also realized that I don't know where anything is on the periodic table besides...uh..most of the first two rows. I don't know what Maggie is going to think on my pre-quiz. If only I could take solely organic chemistry classes...

I had a minor flip out about not being mathematically prepared enough for stat therm after working through some calculus review Dan gave us. Also not knowing how to do double partial dervitives with respect to different variables. He sat me down and showed me how to do it and assured me that the calculus would not be my problem--it would be the algebra and the concepts and that I had a decent grasp, even of partial derivitives. I also had an involved conversation with Alan about various things, including things posted the other day, and about how he and his wife coordinated their careers.

I feel so much more at home in the chemistry department than in the biology department like 99% of the time.

Musings about being a woman in science

Again, the fact that I have so much time and intellectual energy to spend writing my thoughts in this blog indicates that it's definitely time for classes to start again (they start again tomorrow...9 am statistical thermodynamics).

One thing I've been thinking about lately is the idea of how difficult it is going to be to have children if I pursue a career in science. Clearly women do it. My roommate's PI at Oregon Health Science University has a daughter. At my school--which is a liberal arts school and not a hardcore research university to be fair--there is one woman chemistry prof who has two children and three women biology biology profs. Only one of the three women biology profs had a son, although one of the three is in her early 30s and just got on tenure track a couple years ago. (Tangentially, it's remarkable how few women faculty members there are in the sciences that is now that I write that out).

People write about how academia is notoriously difficult for women if they want to have a family because there is no good time to get pregnant. By the time you finish your PhD and post-doc, you're already in your early 30s and not in a position of job security. I've heard of people having kids while they are in graduate school, but usually men. My friend and his brother grew up as little kids on graduate stipends (he said his parents always felt guilty about being unable to provide for them well, but they felt like having macaroni and cheese for dinner every night was awesome--you don't notice when you're a little kid). But the thing is there's no way in hell it would be responsible to carry a fetus while doing lab work, especially in synthetic organic chemistry. I mean, I'm just thinking about the amount of chloroform I inhale while running a column, even when using the hood correctly. That means that you have to take, essentially, a whole year off of working if you want to have children. I'm not sure how other careers--like industry careers--are affected.

My mother was an environmental scientists and worked for the EPA when she had me and she basically worked throughout her pregnancy. She at one point did toxicology stuff and would go to the dump to take samples, but she did other office-based work as well that allowed her to do work that one can safely do while pregnant when she had me. After my brother was born she took time off and returned briefly when we got older, but stopped working again when we moved when my dad got another job. She's now an artist and works on Go Green Wilmette, the local environmental effort in the town we live in, a suburb of Chicago. She said that she sometimes feels guilty for not providing a better model for a working mother, and that we don't understand that the field she was working in was highly male-dominated and that she was one of very few women to work in environmental science in the '80s.

She said on the other hand, though, she didn't want us to be raised by nannies. If she was going to have children, she was going to do it right. I grew up in DC until we moved when I was ten, and there are plenty of families with two parents that had high powered jobs and I knew plenty of kids who saw more of and were more attached to their babysitters than their parents. I have a lot of respect for my mother, and I don't think her choice was a bad one or a weak one. I think that I was raised well, that my parents are intellectually curious people who instilled some of that curiosity in me, and that, although I don't agree with 100% of their parenting choices, they are a pretty good model for how I want to raise my children someday.

I'm at a stage in my life right now, unlike some of my friends, where I don't have a serious long-term relationship yet. A few of my friends are trying to coordinate post-graduation plans (whether it is grad school, Teach for America, or employment) and while enough of them manage to work it out, it seems to be a huge headache--especially for graduate school. One or the other person usually has to compromise or else they're doing long distance for 5 years, and I imagine it doesn't get any easier after that. One of my chemistry profs and his wife worked it out nicely where he works at Reed and she works at Portland State University and they have children and each have tenure. Two of my friends worked it out for REU programs last summer, but it was stressful and one of them had to compromise by going to a (very good but) less competitive program than the best one she got into. It gave them a serious taste of how it would be when they both applied for PhD programs...

More of the girls I know--even as an undergrads--are paranoid about planning their lives and their careers. We think about these consequences way more than our male peers, and we wonder about how taking a path that takes a lot of training--like getting a PhD--affects having a family. This is the main argument I see for jumping into grad school directly out of undergrad.

Edited to add: this New York Times article has some interesting statistics. Excerpt:

Surveying outcomes for 160,000 Ph.D. recipients across the United States, the researchers determined that 70 percent of male tenured professors were married with children, compared with only 44 percent of their tenured female colleagues. Twelve years or more after receiving their doctorates, tenured women were more than twice as likely as tenured men to be single and significantly more likely to be divorced. And lest all of this look like “personal choice,” when the researchers asked 8,700 faculty members in the University of California system about family and work issues, nearly 40 percent of the women agreed with the statement, “I had fewer children than I wanted,” compared with less than 20 percent of the men. The take-home message, Dr. Mason said in a telephone interview, is, “Men can have it all, but women can’t.”

Also, this article addresses the issue with some interesting data on it as well.

Eh, future

Posts like these make me scared--because being a "jack of all trades, master of none" is basically what I have been on track to be through all of my undergraduate education (this whole BMB business with extra chemistry classes). The PI who I sent my CV to who I will be working for this summer saw this as a good thing; he was impressed by my desire to do interdisciplinary research and my varied experiences in the lab. At Reed no one in the chemistry department seems to remember whether I'm a chemistry major or a BMB major because I spent the summer doing organic synthesis. I've been skating between the two departments and following my academic wanderlust since I got to college, and imagine myself doing the same afterwards.

But I worry. I have a few subjects that I am strong in and can be very enthusiastic, but I'm aware that the world is full of people smarter than me. My main strengths are enthusiasm, my breadth of curiosity, and the ability to get very interested in projects. I'm a good student, but not a great student and my transcript is far from perfect. I'm not really cutthroat and when I do well it's because I find some little area that interests me and just dive into it. There's a couple issues at play here: I know I love science enough to want pursue it further but a) do I look good enough on paper to get into good graduate programs? b) where is my place in the scientific community going to be? and c) am I of a competitive enough disposition?

While I feel like I have as solid of a training in organic chemistry as a chemistry major (what classes will I be missing when I graduate? quantum chem and physical chemistry lab) and as solid training in molecular biology as a biology major (I'm missing the population/organismal/evolutionary class requirement), I'm just definitely not (at least right now) approaching it in the traditional "get a grounding in one field and diversify from there" approach at all. The "what the fuck am I doing with my life" question is one I've thought about a lot, and generally all this sorts itself out so I'm not that concerned. But it seems like everyone has a different opinion on what the best way to go in the interdisciplinary sciences is in terms of training, where everything is headed, etc. Also--this is just undergrad--my professor likes to tell us that he studied chemistry (primarily inorganic) in undergrad, got a PhD in organic chemistry, did his postdoc in a physical chemistry group, and now teaches biochemistry and likes to emphasize that--at least in academia--you're constantly re-inventing yourself. My profs keep telling me that no one cares what your degree is called--they care about your research experience and coursework.

I also know I have a full year and a half of school left to ponder these things, and I will likely take time off after that. Fretting is not really productive, and life is full of surprises and changes of plans.

Coffee: good for your brain

And now for some science in the news: Drinking 3-5 cups of coffee a day leads to a lower risk of dementia later in life! It decreases your risk of Alzheimer's and has also been associated with a lower risk of type 2 diabetes and Parkinson's.

I love reading articles extolling the benefits of my deep addiction.

Polyketides again

I've been thinking lately that I would like to go into polyketide chemistry, lately. I'm going to work in a lab this summer that works with bacterial polyketides, and as far as I can tell, the whole field pretty much brings my all my interests together. Even in light of what I said about combinatorial chemistry (and in this case, biology) which is an aspect of playing around with biosynthetic genes.

It's one area of chemical biology that has caught my interest this year (which is basically when I started browsing the chemical biology lit). It relies heavily on organic and bioorganic chemistry, but also genetics and even tracing evolutionary pathways (like this review that talks about how the classifications of polyketide synthases are a little rigid). There's a med chem/natural products discovery aspect to it, since a lot of these structures are really promising medicinally as antibiotics and chemotherapeutic agents (and like I posted yesterday, the genome-mining approach). There's a synthetic organic aspect because a lot of these structures are good targets for total syntheses due to their medicinal qualities. There's an enzymology aspect because a lot of these biosynthetic enzymes have really interesting proprieties. And then there's even some work on trying to harness enzymes that do mechanistically biosynthetic transformations hard to emulate with classical reagents for use in total synthesis, like this total chemoenzymatic synthesis. There's a structural biology aspect too--like this paper looking the structural basis for polyketide synthases docking and substrate specificity. I suspected there would be some biomimetic organic synthesis based on some of these bacterial polyketide biosynthetic pathways out there, and a quick google search told me that there's is, indeed, loads of work being done in that area.

I've started bookmarking webages of labs that publish in this area (and other areas that look interesting) because...well, I figure if I still want to go into this (kind of specialized) area by the time I decide to apply to grad school in a couple years, that's probably a decent approach. It just seems like such a promising area for me and for my desire to bring all these interests of mine together. And just to see where it goes generally. It's not a cutting-edge new field, but just a field that keeps getting cooler and cooler as our tools to do science get cooler and cooler.

Knowing vs. Finding Information

One thing I think my generation is very good at is finding information. Not necessarily knowing information off hand, but being able to sift through search engines and databases and find what we want. People of my parents' generation keep complaining that we can't do basic math, we can't spell, and our handwriting is atrocious. But my parents are amazed at the speed at which I can retrieve information off the Internet. (Part of it is that I waste an atrocious amount of time browsing--but I do discover a lot of new neat shortcut Internet applets and webpages this way).

Now in light of science education and science as a whole, I'm not sure where this puts us. I have a really hit or miss memory (I either know extremely detailed information or I totally blank out), and memorizing enough information to do well on exams is a chore. I mean, I'm glad I was asked to memorize the amino acids in biochemistry, enough basic organic reactions, and enough pKas to be able to guesstimate most pKas of organic materials because it does help with my fluidity in understanding papers and talks. It's not that I'm incapable of memorization--I'll do it. I'm supposedly "good" at things that people traditionally associate with being memorization heavy, which I contest are more problem solving. In fact, the way I studied organic chemistry was by stringing together the reactions in goofy synthesis problems of partial structures of psychedelics that I looked up on wikipedia or just some molecule I thought looked cool that I made up. I would make up practice problems for my friends--and this would give me a chance to think about the problems retrosynthetically and when I got to a problem on a test I was used to thinking about a variety of sequences that would be useful for making and breaking bonds and had several strategies for this laid out in my head. I talk to a lot of my classmates who also did well in that class and most of them tended to take a more conventional flash card and practice problem approach. I did some practice problems and flash cards, sure, but every now and then I needed to make it more of a game to maintain my interest. It probably has something to do with my ADHD--I try to turn studying into games because when I'm engaged I go into hyperfocus mode which is really conducive to studying, writing papers, or lab work (ADHD can be a curse, but also a blessing). This is a tangent, though.

My ability to retrieve information came especially in handy in my advanced synthetic organic course when all of our exams were open book and taken straight out of the lit. The problems, then, were extremely difficult, but that meant that I could focus on categorizing information and developing strategies in my head for how to put it together rather than storing it, which is much better for my learning style.

Given the great abundance of information available to us, I'm not even sure that knowing information off-hand is even all that useful--especially in very interdisciplinary fields. I think it's more important to be aware that information exists and then be able to retrieve it quickly or ask another person who is an expert. Learning how to critically think, to research, to evaluate, and to organize information is important when you have endless sources of it at your finger tips.

Honing these skills, obviously, is not always a practical approach for a lot of classes geared at giving you a basic background in the subject, though, and I'm not sure how to reconcile this. I also see how you should very detailed information about a project you are very close to, like a thesis. But in terms of a general knowledge base of scientific literacy? I still contest that it's more important to know how to find information in this day and age.

Incidentally, a friend of mine who is a classicist said similar issues came up in their field when the Perseus Project went up. It meant that they didn't necessarily need to memorize as many strict grammatical rules and vocabulary since it was hyperlinked in the text, and revolutionized the way students would go about reading ancient texts. So the question of "how much information is necessary to hold in your head compared to what has conventionally been deemed necessary" is not unique to science. I guess in some ways it's akin to the fact that people stopped memorizing whole epics to perform orally after the printing press allowed books to become widely available and people talked of the demise of the oral tradition. In reality it just led to a whole new set of opportunities in literature.

Genome Mining for Natural Products

I've discovered a lot of interesting science in ChemBioChem, a European chemical biology journal. We have more access to more of these journals than most of the Nature journals; it must be because there is some relatively cheap Wiley journal package that comes with Angewandte Chemie, since we basically get all of the European chemistry journals that are published by that group.

But in any case, one pet area that has been fascinating me lately is the convergence of genetics, microbiology, analytical chemistry, and synthetic chemistry to the discovery of new natural products, especially in examining modular biosynthetic polyketide genes. This review that came out a few days ago, Strategies for Discovering New Natural Products through Genome Mining, went through basically what is being done in the field.

The authors explain that natural products discovery has not been favored by pharmaceutical industries for a while as a way to discover new drugs. Most of the 20th century (after penicillin was discovered) is described as the golden age of antibiotics and natural product discovery. It has fallen out of favor because it is time intensive and often leads to discovery of natural products that are already known.

But now, in a post genomics era with so much bioinformatic data out there, we actually have new strategies to approach discovering natural products, especially in examining biosynthetic gene clusters. We can search for PKS (polyketide synthase) domains, we can knockdown genes, and (most exciting to me) you can reconstruct products in vitro to determine if that gene cluster is actually making what you think it is (and then confirm what you have with NMR and MS). Of course, with the reconstruction strategy there are certain problems, like finding the right promoter and so forth, but chemoenzymatic total synthesis to reconstruct biosynthetic pathways has been done in vitro before.

Polyketides are neat from a pharmacological standpoint, because the secondary metabolites tend to have a lot of medicinal properties. They are also neat in that a lot of the genes are modular, so there have been some papers where they re-arrange them essentially doing synthetic chemistry in a cell instead of in an RBF. And sometimes they have neat little genes beyond just PKS genes--I recently wrote a paper for school reviewing research on a gene that was responsible for doing a powerful oxidation to form a chiral THF ring. It seems like a way to both discover new natural products with pharmaceutical value and to generally get a better mechanistic grasp of biosynthesis.

Combinatorial Chem

I've been reading about combinatorial chemistry lately, especially its applications in drug discovery. Last semester Jordan Katz (a Reed alum who recently finished his PhD) gave a talk about using a combinatorial approach to find the right inorganic materials for solar cells--unrelated to drug discovery, but showing that it is a useful technique in a variety of applications. This paper and this paper aren't exactly new, but they were my first introduction to the idea of screening a modular library that utilized a combinatorial approach (papers read in my topics in biochemistry course this past fall).

I think I understand the utility of such an approach. Biological systems are complicated, and the idea of design feels really...strange in some ways. Nature works through selection, not design. I know that there are drugs that have been designed, but I can see how a combinatorial approach would be a useful angle since there are so many potential compounds that could be pharmacologically active (is "chemical space" the right term?).

But every time I read a paper that uses a combinatorial approach, all I can think is how boring it must be for the poor grad student or lab tech carrying it out, since it's a conceptual problem that takes a lot of hands going through tedium to sort through. I think at an abstract level, design is more appealing because it is just more satisfying conceptually to think through a rational structure. At least, as a reader, it's more satisfying to read about. I can't help but find combinatorial chemistry boring, however useful of a tool it may be.

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.

Liberal Arts College vs. University

I am very much a proponent for a small liberal arts school science education. I have no idea how I will fare later in life, but I have no doubts that my education has been anything but excellent, and, on the whole, superior to my friends' educations that go to large institutions.

See, even here I had some large lecture-based classes that kind of sucked. Introductory chemistry was ~120 people. However, even with 120 people in the course it was a) taught by a professor b) all our exams were graded by him (even if he hired student graders for homework and lab reports) and c) he knew every one of our names. Even then he was down for p-set help and just dropping by his office to chat. And this particular professor is what drew me into the chemistry department in the first place. Later my courses got smaller and more specialized, and I suppose that is the case anywhere.

My friends at Berkeley, University of Illinois, and other large research-focused institutions describe to me gen chem and even organic chem classes as being ~500 people. My sophomore organic class was 70 people, and this was considered abnormally large (usually it's closer to 50), and definitely much larger than the average Reed class. They also describe this trend towards making it more interactive involving clickers that digitally record answers to multiple choice questions on the screen, which in reality is an easy way for the TA to take attendance (which I think is silly; we're all adults now, the only person you're hurting is yourself--unless you don't get anything from going to lecture anyway--and then what's the point?). Students get around this by getting their friends to go to class and press their respective clickers for them, and take turns who goes to class just to press the clicker enough to get participation points.

My friend Luke is in the aerospace engineering program at the University of Illinois--which is a great program, one of the best in the country--and he says the big advantage is that in a couple labs they got to go see real planes and play with the mechanics. You just don't have those sorts of facilities at a smaller institution. But he said he also did not know a professor well enough to ask for a recommendation when applying to summer programs and he has no clue what he is going to do when applying to graduate school. He said that he often feels that the access to larger facilities in the end doesn't outweigh the benefits of having mentors relationships with professors who know you personally considering how infrequent access to these facilities are.

I know I certainly complain enough about Reed not having subscriptions to Nature Chemical Biology or Nature Reviews Drug Discovery, and I would have access to that at someplace like, say, Berkeley. I also know that if you are an undergrad confident, savvy, and lucky enough to ask and land a research position then you get to do things that we can't do here. Our science is modest; sound in methodology, but far from cutting edge. Profs publish, some more than others, but not that often. I know that if you are bright and self-directed you can make use of the facilities and resources of being in a larger institution, but in all honesty, it seems like most undergrads get lost in the sea. It also seems like anyone who is extremely self-directed does a fair bit of teaching themselves things; and while I'm all for self-teaching, it makes me question what the point of having class is. If the syllabus is online, if you have libraries full of books and journals to read, and if you can check your answers against an answer key, no wonder people at larger schools skip class. I always found that self-directed learning is great, but complemented by really excellent teachers.

I am sure there are some students who are better equipped to deal with bigness than I am. But I feel like for most of us, we're still figuring our shit out and we need more interaction to keep us from just skating through. I feel like I am solidly accountable for my work, and no one is just shuffling me through the system, and like I am getting trained to think like a scientist. Yeah, Berkeley has some sweet facilities, but it's not like I would get a chance to use them as an undergrad in all likelihood anyway.

Flourescent Protein Timers

Since Reed doesn't have a subscription to Nature Chemical Biology (I guess I could Interlibrary loan it if I'm really curious--but I still find that incredibly annoying), I'm stuck reading other blogger's accounts of the cool research in there. Like florescent proteins that work as a timer. As far as I can tell, they change color temporally, making them potentially a really powerful tool for cellular tagging and localization studies.

Seriously, though

Apologies for posting here so much; I'm on the last few days of winter break and have the time to do so, I suppose and I'm going a little stirr-crazy.

I was wondering if there are better RSS feeds than the one I have for PNAS, Nature, and Science. All of my ACS journal feeds are quite nice; it gives a full abstract as well as a graphical abstract and makes browsing really easy. And I recently managed to dig up a better feed for Angewandte Chemie (mostly due to reading chemistry blogs of other science people who spend far too much of their life on the interwebs). But I can't find an RSS feed for Cell, and Nature, PNAS and Science suck. No abstract, no nothing but the title and authors. Do biologists spend less time dicking around on the internet? I doubt it. There is way too much down time in molecular biology for that to be true. I gotta do some surfing around to find them.

Unrelated, but I also found it interesting that there was an extensive review article about RNA interference in Angewandte Chemie the other day. The borders of biology and chemistry are becoming very fuzzy indeed.

On Chemical Biology

So I think I mentioned earlier that I'm pretty sure I don't want to go into traditional biochemistry or structural biology because it's not exactly biology-meets-chemistry, it's kind of it's own thing. Here's excerpts from a PDF that I found on the UCSF website somewhere on one of their chemical biology pages:

Is there a problem?
Chemistry is a very mature science compared to biology.
Chemistry graduates continue to grow overall but at modest rates compared to biology graduates. What is making this happen?

...

What is Chemical Biology?
A paradigm shift in allowing scientists systematic access to chemical tools to probe important problems in biology.
It is not the same as biochemistry which uses chemical principles to probe biological molecules.
It is not the same as chemistry which is focused on synthesis and properties of small molecules.
It is not the same as molecular biology which modifies biomolecules to probe cells.

...

"It is different than molecular biology with the use of small molecules to probe biology offering numerous advantages to gene knockout and siRNA knock- downs, the modern tools used by molecular biologists. Proteins contain multiple functional sites and these"ablative tools" do not allow one to dissect individual functions. Moreover, cell signaling events occur quickly often with time-scales on the order of minutes. siRNA usually requires >24 hours to have its maximal effect and even then it usually only ablates 60-80% of the protein. Gene knockouts represent constitutive inactivation, unlike the acute inactivation that can be generated by a small molecule. Not surprisingly these different probes often generated different results. Small molecules represent rapid and dose-dependent probes of cellular function and the information that is generated is more relevant to drug discovery."

This is all very appealing to me. I'm all about small molecules and how they apply to biological systems. That, in my mind, is chemistry-meets-biology. I guess my main problem was that I read a lot of chemical biology papers that felt very...artificial. I think I describe it as "interdisciplinary for the sake of being interdisciplinary rather than having a point" somewhere on this blog, if not, if you know me in person those words definitely have come out of my mouth.

But I guess a lot of that has to do with the fact that trying to define chemical biology as a field is pretty new. I mean, the essence of what it is has been around for a long time called by different names. There has always been a chemistry-biology interface and medicinal chemistry has always been on it; this isn't exactly new. But defining this interface as a true discipline is, and trying to work more on the interplay between in vitro and in vivo with small molecules is definitely new.

I just need to find a corner of it that I feel like has a point and not, like, spend my life making aptamers that will never ever compete with real antibodies unless I find them to be extremely structurally interesting. Not that that is exactly a waste of time per say, just it doesn't seem satisfying to me. There's a lot of room to grow in this discipline, and I think interdisciplinary science is the way of the future.

Molecular imaging

The article in PNAS about using magnetic resonance to visualize a virus (which I originally heard about from Derek Lowe's blog In the Pipeline) seems to hit everywhere. I saw it in Nature News, and even in the New York Times. If you look at the image side to side with the electron micrograph, the quality of the image is spectacular. There's even talk about the idea of single-cell MRIs not being too far out of the realm of possibilities in the next ten, twenty years. Wouldn't that be fantastic?

It makes me wonder if crystallography is going to become obsolete at some point in my lifetime. Getting proteins to crystallize is time consuming and difficult (not that I have ever done it!). Not all proteins crystallize and then there's the whole issue of whether the crystallized conformation is really even biologically relevant or whether the crystal is good enough to justify a model, etc. etc. If biophysical imaging techniques at the nanoscale keep getting better and better, who knows what we'll be able to do in structural biology. All that time and energy spent trying to crystallize a protein can be spent studying structure at a different level. It could even be like the boom in the complexity of synthetic organic chemistry and natural products synth after high resolution NMR became widely available.

Maybe being able to read NMR spectra all together will become obsolete and we'll just pull up 3D images of the compounds on the computer after making something in lab. Who knows.

The scientific world is going to be so fantastic by the time I get to really enter it.

Education

There seems to be two camps of thinking about course decisions in my major. Biochem majors have a lot of requirements; it's the nature of being interdisciplinary. Some people in my major say "I'm probably going to grad school, I'm probably going to be thinking about science for the rest of my life and in a lab for the rest of my life, while I'm in undergrad I might as well take as much liberal arts stuff as I can." This seems legit, and this seems like where I thought I would be. After all, I'm the one who nearly didn't take gen chem my freshman year because I was ambivalent about the idea of studying science at a liberal arts school (and thought I was going to be just a biology major since I abhorred chemistry in high school). I get where that side's coming from.

But somehow, somewhere along the lines, I changed. I can't get enough science coursework. It's very strange. Every semester, there's another elective class that really want to take. Last semester I took advanced synthetic organic and a biochemistry seminar that fulfilled no graduation requirements. Next semester I'm taking advanced mechanistic organic, intro inorganic, and a biology seminar all of which do not fulfill any requirements. What is wrong with me? Am I becoming unbalanced?

And here's the thing: I love literature. I love music. I love history. I'd like to take some economics. I took a great religion class freshman year. I read novels and non-fiction unrelated to science voraciously during breaks. I like liberal arts classes, and there are any number of other things I am interested in beyond chemistry and biology.

So what changed? I guess part of it has to do with slogging through so much intro coursework to get here. Intro bio, intro chem, intro physics, even organic (as much as I liked it) was essentially an intro class. Now I am finally qualified to take small upper-level courses in my major with people who are serious about the subject matter, especially in elective courses. I know the professors and they know me, and it is all around a great experience usually. Seminars are great because they are more like journal clubs than classes. But you can't take those sorts of classes until you have the background.

The other thing is that I'm just do damn interested in everything. I seriously wish I could double chemistry & biology. It's the same side of me that wishes I could take everything under the sun that is not science that wants to take everything I can take in the two departments. Of courses, taking everything I would like to take is just simply impossible, but so it goes.

I'm also still discovering what exactly my scientific interests actually are. There's so much I just simply do not know, and the more I learn, the more I figure out what exactly it is that grabs me. For example, realizing that biochemistry is kind of it's own thing, and not exactly biology-meets-chemistry. Which is fine, great to learn about, and not what I want to do ultimately.

Sometimes I wonder, though, if I am jipping myself out of my last shot at taking liberal arts courses?

More on Watson

Actually, I take some of that last post back. Tying in that old reference from Chargoff that everyone else had forgotten was pretty clever. Also, saying that Linus Pauling's three helix model was a bunch of BS took balls (I mean, seriously, he's Linus Pauling). I guess he did have several moments of important insight that took the biophysical and biochemical data to incorporate it into a coherent model. I guess I shouldn't necessarily undervalue the big picture thinking. (I think I tend to do that because I tend to see big picture more intuitively than little details, and I immediately assume that the little details are always undervalued because they are harder for me personally. I suppose there are other people who feel like it's the opposite.)

He also took back some of what he said about Rosalind Franklin:

Rosy showed Francis her data, and for the first time he was able to see how foolproof was her assertion that the sugar-phosphate backbone was on the outside of the molecule. Her past uncompromising statements on this matter thus reflected first-rate science, not the outpourings of a misguided feminist.

Obviously affecting Rosy's transformation [in regards to the acceptance of the double helix model, which she had previously vehemently opposed] was her appreciation that our past hooting about model building represented a serious approach to science, not the easy resort of slackers who wanted to avoid the hard work necessitated by an honest scientific career. It also became apart that Rosy's difficulties with Maurice and Randall were connected with her understandable need for being an equal to the people she worked with. Son after her entry to the King's lab, she ad rebelled against its hierarchical character, taking offense because her first-rate crystallographic ability was not given formal recognition.

...Since my initial impressions of her, both scientific and personal (as recorded in early pages of this book) were often wrong, I want to say something of her achievements. The X-ray work she did at King's is increasingly regarded as superb. The sorting out of A forms and B forms, by itself, would have made her reputation; even better was her 1952 demonstration using Patterson superposition methods, that the phosphate group must be on the outside of the DNA molecule...

...we both [he and Crick] came to appreciate her great personal honesty and generosity, realizing years too late the struggles that the intelligent woman faces to be accepted by a scientific world which often regards women as mere diversions from serious thinking. Rosalind's exemplary courage and integrity where apparent to all, when, knowing she was mortally ill, she did not complain but continued working on a high level until a few weeks before her death.

Still a sexist (the woman had to prove herself to not only be competent, but first-rate, to be taken at all seriously), but the memoir was also meant to be told to reflect how they went through the process of figuring out the structure of the double helix, and those were his first impressions of her.

Interesting fellow, even if he is a raging bigot.

On Watson, Sexism, and Intellectual Laziness

I'm reading James Watson's account of discovering the structure of DNA with Francis Crick in his memoir The Double Helix. Watson has always struck me as kind of a racist d-bag, and I know part of it is being a man of his times. But the sexism is also killing me, just in how he talks about Rosalind Franklin:

...Maurice, a beginner in X-ray diffraction work, wanted some professional help and hoped that Rosy, a trained crystallographer, could speed up his research. Rosy, however, did not see the situation this way. She claimed that she had been given DNA for her own problem and would not think of herself as Maurice's assistant.

I suspect that in the beginning Maurice hoped that Rosy would calm down. Yet mere inspection suggested she would not easily bend. By choice she did not emphasize her feminine qualities. Though her features were strong, she was not unattractive and might have been quite stunning had she ever taken even a mild interest in clothes. This she did not. There was never lipstick to contrast with her straight black hair, while at the age of thirty-one her dresses showed all the imagination of English blue-stocking adolescents. So it was quite easy to imagine her the product of an unsatisfied mother who unduly stressed the desirability of professional careers that could save bright girls from dull marriages to dull men...

Clearly Rosy had to go or be put in her place. The former was obviously preferable because, given her belligerent moods, it would be very difficult for Maurice to maintain a dominant position that would allow him to think unhindered about DNA. Not that at times he didn't see some reason for her complaints--King's had two combination rooms, one for me, the other for women, certainly a thing of the past. But he was not responsible and it was no pleasure to bear the cross for the added barb that the women's combination room had remained dingily pokey whereas money had been spent to make life agreeable for him and his friends when they had their morning coffee.

Unfortunately, Maurice could not see any decent way to give Rosy the boot. To start she had been given to think she had a position for several years. Also, there was no denying she had a good brain. If she could only keep her emotions under control, there would be a good chance she could really help him...

...The real problem-then, was Rosy. The thought could not be avoided that the best home for a feminist was in another person's lab.

...Naturally I was delighted when Maurice said I would be welcome at Rosy's talk. For the first time I had a real incentive to learn some crystallography: I did not want Rosy to speak over my head.

We have certainly come a long way, that's for sure in terms of women in the sciences. I know sexism still exists (especially in regards to getting a post-doc and tenure with respect to wanting to have a family), but thank god for scientists like Franklin who cleared the way for us today.

The other thing that bothers me about Watson is that he seems intellectually lazy. He describes himself as a "mathematically deficient biologist" and claims to have never taken any organic chemistry or advanced chemistry or physics in college at all:

My interest in DNA had grown out of a desire, first picked up while a senior in college, to learn what the gene was. Later, in graduate school, it was my hope that the gene might be solved without my learning any chemistry. This wish partially arose from laziness since as an undergraduate at the University of Chicago, I was principally interested in birds and managed to avoid taking any chemistry or physics courses which looked of even medium difficulty. Briefly, the Indiana biochemists encouraged me to learn organic chemistry, but after I used a Bunsen burner to warm up some benzene, I was relieved from further true chemistry. It was safer to turn out an uneducated Ph.D. than to risk another explosion.

He goes on and on about how Crick understood the math and theory behind crystallography, and how he only acquainted himself with it on descriptive terms because it bored him to learn anything about biophysics or biochemistry. He talks about how studying the metabolism of the bases is boring, and how basically all biochemistry and organic chemistry is boring unless it applies to the gene.

He makes a good point when he talks about Linus' Pauling's discovery of the alpha-helix, which Pauling did on descriptive terms before confirming it theoretically; that playing with modeling kits and pictures can be a useful way to understand structural biochemistry and biophysics. It's not inherently the fact that he relies on descriptive terms that bothers me. After all, I operate on a diagrammatic, descriptive level and am aware of the fact that I don't understand most of the math that the computer does for me. A professor that came to give a chem talk at Reed once made the good point that you don't need to understand hardcore physical and quantum chemistry to have a good chemical intuition about reactivity; for example, understanding steric hindrance, ring strain, and favorable conformations are all things we tend to do at a descriptive level, even if there are computational reasons to back up the chemical intuition. So some scientists are quantitative types and others are more qualitative types, and yeah, it takes all different types to solve problems in science, fine. It's just this total irreverence for the fact that other fields are interesting and worth learning about that gets to me. I hate intellectual laziness. It's one thing to be deficient in some areas in your background--no one knows everything. It's a completely different to not be intellectually curious enough to want to know more about things you don't know much about.

Watson doesn't really seem like a complete genius. He seems like a guy who was really really into this one pet issue and was determined and lucky enough to fall into a crowd of exciting and talented people (like Crick, Rosalind Franklin, and Linus Pauling) who actually were brilliant. It angers me that Watson can be such a bumfuck, and Rosalind Franklin can be off in the lab, being brilliant, giving herself cancer, only to be viewed as a tool for the boys to understand DNA. She made it her project because she wanted to understand the structure of DNA too, not because she was trying to be spiteful and difficult. They just assume that they can use her expertise and her intellectual contributions as if she is just technical support.

This book is fascinating from a history of science perspective because he writes in his unabashedly caddish way about it all. About the politics and personalities of these people you read about in textbooks. About a time when science was even more of an old boys club than it is now.

Also, maybe you don't need to be brilliant to be a Nobel laureate, you just need to be mildly creative and fall into a good in-crowd.

On Reading the Lit

I don't read journal articles for fun the way I do for class--where I sit down and try to understand as much as I can, devoting hours to reading a single article. I read them just to be swept in awe by the overwhelming amount of fantastic science being done right now, browsing through, clicking around, mostly skimming abstracts and figures. Mostly I find myself reading biological chemistry and organic chemistry. And lately biophysics (mostly just the abstract and introduction because I really don't understand the math behind it). Some of the biophysical techniques that are going on...I can't even imagine how fantastic the scientific world is going to be in 10 or 20 years. For example, they can do NMR imaging of a virus now.

I read a review of total synthesis in the last hundred years and how far it has advanced. And docking carbohydrate synthesis on DNA as a way to functionalize microchips. And each leads to references to wander to, letting my mind wander and skim and wander and skim.

I'm realizing that it's now getting to be time to start actually keeping up with the lit--even if it is just skimming every few weeks, or even if it's just reading C&E News and/or review journals. Since there's so much out there and no one can read everything, my professors are reading the same journals, they've just been doing it for longer and with more specialized interests.

I finally have the background to get a vague sense of what articles in the current lit (at least in organic chemistry, biological chemistry, some of the more qualitative aspects of biophysics, biochemistry, and cellular & molecular biology) are about, even if I don't fully understand them, and learning about science isn't going to be spoon-fed to me through assignments for the rest of my life. It's time to start getting into the habit of reading journals like it's time to get in the habit of reading the newspaper. Not cover to cover, not necessarily every day (or even every week--after all, I still am a student), but as something I do periodically.

On Stupidity

My roommate's thesis advisor sent her a link to the following article The Importance of Stupidity in Scientific Research. It was interesting to read, because I think it is absolutely true.

Second, we don't do a good enough job of teaching our students how to be productively stupid – that is, if we don't feel stupid it means we're not really trying. I'm not talking about `relative stupidity', in which the other students in the class actually read the material, think about it and ace the exam, whereas you don't. I'm also not talking about bright people who might be working in areas that don't match their talents. Science involves confronting our `absolute stupidity'. That kind of stupidity is an existential fact, inherent in our efforts to push our way into the unknown. Preliminary and thesis exams have the right idea when the faculty committee pushes until the student starts getting the answers wrong or gives up and says, `I don't know'. The point of the exam isn't to see if the student gets all the answers right. If they do, it's the faculty who failed the exam. The point is to identify the student's weaknesses, partly to see where they need to invest some effort and partly to see whether the student's knowledge fails at a sufficiently high level that they are ready to take on a research project.

Productive stupidity means being ignorant by choice. Focusing on important questions puts us in the awkward position of being ignorant. One of the beautiful things about science is that it allows us to bumble along, getting it wrong time after time, and feel perfectly fine as long as we learn something each time. No doubt, this can be difficult for students who are accustomed to getting the answers right. No doubt, reasonable levels of confidence and emotional resilience help, but I think scientific education might do more to ease what is a very big transition: from learning what other people once discovered to making your own discoveries. The more comfortable we become with being stupid, the deeper we will wade into the unknown and the more likely we are to make big discoveries.


I think Reed is actually abnormally good at making you feel very small and very stupid. Even if it's not quite the same as research, the classes are geared towards giving you problems in the current literature and making you think about them in novel ways. My organic chemistry tests and biochemistry tests were not dependent on just knowing the information, but also knowing the information and learning how to apply it to a new setting. We also spend a lot of time sifting through the literature in upper level classes, and you get a sense that you are very small and there is a whole unknown, unsolved world out there. On top of which, we have an unusual grading policy where we are not shown letter grades for the work we do; we are assigned letter grades for our classes, but to see them we have to ask our advisor, and we are only informed if we performed above a C which is "satisfactory" when we receive reports at the end of the semester. You see numbers, you see correct or incorrect answers on exams, you get comments on written assignments, but you never know exactly how well or poorly you did, just an overall sense, which is often skewed anyway. I also struggled with my intros, and didn't really start to do well until I hit my upper level classes, so I dealt with a lot of academic failure and feeling stupid in my time. And even so; it didn't end there. In advanced synth a class I did very well in, Pat assigned us problems that he didn't even expect us to get correct. I mean, sometimes I did but mostly I didn't. The point was learning a process of solving problems and to demonstrate that you have picked up that process. The point was just to grapple through some really tricky questions that are a little bit above your current level.

The school also pushes you to your limit emotionally; I feel intellectually accountable for my work, and like when I'm not doing it well I'm actually disappointing my professors. Basically, Reed College makes me feel very stupid, even when I'm doing well. I feel like there's always more I could be doing, more I could be learning, more about every topic I should know. This is not quite the same as addressing new, unknown problems (hell, the known ones are intimidating enough), but the feeling that I'm stupid is something I am very used to, and embrace. I've even heard the phrase "if you don't feel stupid all the time at Reed, you're not doing it right".

The world is a big place with a lot of smart people in it. No, I'm not a super genius, and in some ways I'm not even that conventionally intelligent (I have trouble with things like standardized exams). I don't mind the idea of failure in lab, because so many things are out of your control. Isn't that the exciting part, muddling through until you figure it out? Tweaking this and that? Few things are as simple as they look on paper. Lab is different from school, which is awesome in my book. It's a whole different set of puzzles. But I like chance games and gambling. Things that involve a lot of skill and a lot of luck. Keeps things exciting.

So what is the big deal about feeling stupid all the time anyway?

Life plans

I've been thinking more and more about graduate school lately, and I'm pretty into the idea of going. I've spent a lot of time not marrying myself to the idea due to a lot of reasons (mostly including self-doubt, a low GPA, a keen awareness of how competitive the world is, and a certain resistance to the idea of doing something just because it's what you are "supposed" to do) and trying to convince myself it's not what I necessarily want, or that I shouldn't close myself off to other options in life or to the idea of not doing it. But when it comes down to it, I want to do science at that level eventually and I know that, and have basically been becoming more and more sure that I love science, I can handle being pushed to my limits with work emotionally, and that I have the drive to work on the sort of project a PhD would be. And while I'm not the best test taker, I have strong skills in other areas. I'm good in the lab, I'm good at communicating ideas face-to-face, I know how to retrieve I don't know quickly on the internet, I can talk about science cogently, I know how to digest the primary lit. I know professors who can attest to these skills.

But then I try to take things in perspective. I'm studying the hard sciences at a hard school. I know several profs who could write me good recommendations. I have a lot of research experience. And a really broad scientific background with a solid academic program. These things all matter too, right? Perhaps matter more than my GPA?

I don't know. It's hard not to worry, but I spend so much time consoling other people that I'm starting to believe my consolations. It is scary. We have this giant recession and everything worth doing, or so it seems, is incredibly competitive. Medicine and law and grad school in most other fields are more competitive, it seems, so maybe I should count my blessings.

But off of this "woe is me, can I hack it?" shit, I think I've finally figured out what I want to study, broadly. Basically, synthetic organic heavy-yet-still-interdisciplinary chemical biology. I want to do something more at the interface of chemistry and biology. The ideal program would be something like (ha! ha! ha! after talking about all this GPA woe) UCSF's Chemistry & Chemical Biology program. As far as I can tell, a lot of this interdisciplinary stuff is under all different labels, so my actual PhD could be in any number of things (including biophysics), it all depends on the individual labs I am interested in. I should start keeping lists of labs that are publishing projects I'm interested in that I come across in the lit.

So this is the plan right now: finish off this year (my junior year) strong, get a another summer of research this next summer (and prep for the GREs), take the GREs next year, then take a year off and apply to grad school during that year, and tech. I've also seriously thought about moving to the Bay Area after Reed, although possibly staying around Portland and trying to get a job at OHSU.

Okay, this moving to the Bay area thing is a recent idea, related to this whole actually I kind of want to go to grad school thing. I visited some friends there who were in biophysics programs at UCSF and Berkeley. Which basically was what made me come to believe that these were the sort of people I wanted to be around and the sort of environment I wanted to be in. We talked about science! Even when we were in the bar! And more science! Some people think this is sad and indicative of an utter lack of ability to fit in socially. Perhaps, but I want to be able to talk about science with my buddies when drunk. The facilities at UCSF blew me away, and the projects they were doing where just so spectacular. The sort of stuff you read about in Nature, but at a small liberal arts school, we just don't even have close to the facilities to do.

But oh yes, I was talking about why I want to move to the Bay after Reed. It's a bigger city than Portland, but one I have ties to. A lot of people I go to school with grew up there, but there are also a lot of Reed alumni who move there for work or grad school, and so there's the sort of safety net of being around Reedies, but the novelty of being in a new city. In addition, I was born there and lived there until I was 2 and a half, and my parents have a lot of family friends who live there, some of their oldest friends from before they were married. There are even a couple friends from high school who went to school out there who might be around. It's not totally restablishing myself in a new city as much as moving other places would be.

Also, as far as I can tell, The Bay area and Boston are the place to be for the biological sciences. There's just such a neat relationship between the academic powerhouses and the biotech industry in those locations that I don't think exists to the same degree elsewhere. I could probably find a job as a tech, people seem to, at least. So at least I could be connected to the science, because I think I would be really unhappy in a situation where I wouldn't be doing science to some degree. Also, San Francisco rocks! The city is gorgeous, the climate is great, there's plenty of hipster culture and coffee snobbery and all that stuff. It's still the Pacific Northwest, which I love. I love the West Coast, and I don't really want to move back to the Midwest or East Coast. It's just a vibes and personality mesh thing. The only concern is that it's expensive to live there and rent is expensive. On the other hand, it's just for a year, maybe 2; I just need to sustain myself, and I'm not looking to save money. I can live reasonably cheaply, and I don't want to live in someplace boring just because it's cheap to live there.

I love Portland. Portland is a neat place to live, and I only got tastes of what it is like to be a person in Portland and not a student who spends her whole life between the library and lab during the school year, but I spent a summer there and got a feel for it, and I really do like the city a lot. It's been good, but after 4 years it's time to see more of the world. The argument to stay in Portland is that I really do have a lot of friends out there and possible employment prospects. It's sort of a comfort zone thing. Also, it's really cheap to live in Portland, and Portland is far from boring, unlike a lot of other cheap places to live. Portland is a great place to be a 20something.

So anyway, that's my current life plan. Finish undergrad, take a year off in the Bay Area, go for the PhD. Narrowing down what exactly I mean by "synthetic organic heavy chemical biology" might be good too. Figuring out if those projects are in Chemistry & Chemical Biology programs, Chemistry programs, Biochemistry programs, Pharmacology programs...

What comes after the PhD? Academia, I think, although industry and a number of other paths aren't out of the picture either. This is a little more hazy. But seriously, I think academia is more my style. My friend and I have a running joke that if we decide in ~10 years and/or during our post-docs that if we're not feeling the academic route, then we're starting up a biotech company together; he thinks there's a 10% chance of that happening. So maybe it's making the big bucks in biotech. In any case, it's something, although I'm not quite sure what.