Sunday, November 30, 2008

PLoS journals

Constance Bailey: http://www.nature.com/nature/journal/v441/n7096/full/441914a.html
Constance Bailey: (sorry, I've been really intregued by the PLoS journals lately)
gvtennis55: hahaha
gvtennis55: i like the title of this article
gvtennis55: 14.7 is legit, dude (14.7 is the impact factor of PLoS biology)
Constance Bailey: http://www.nature.com/nature/journal/v425/n6958/full/425554a.html
Constance Bailey: yeah
Constance Bailey: i mean, it seems to have legit science
Constance Bailey: and so forth
Constance Bailey: just it's running itself bankrupt
gvtennis55: dude that would suck if you published in this journal
gvtennis55: and then they were no more
gvtennis55: IF of zero motherfuckers!
gvtennis55: also, what's up with this nature article about how it's competitor will ultimately fail with their competing business model?
gvtennis55: because if nature can convince enough authors that this PloS won't be around, nobody will submit and the prophecy will come true
Constance Bailey: it's like the NPR/PBS of science journals
Constance Bailey: i like it
gvtennis55: i know yo udo
gvtennis55: (you also like NPR)
Constance Bailey: they should do pledge drives
Constance Bailey: take the NPR business model
gvtennis55: hahahahaha
gvtennis55: you mean embrace what this article says they should run from - a permanent reliance on philanthropy?
Constance Bailey: "donate 100 dollars to PLoS and we will give you this limited time PLoS logo 1,000 mL micropipette"

Saturday, November 29, 2008

AHHHHHHHH. The end of the semester. It's hectic. Writing a bunch of papers, final lab reports, have my final exams coming around the corner. So much work left to do for my synth final--I need to write a paper and then be prepared for an oral grilling.

I'm midway through a paper on inducible nitric oxide synthase's role in type 1 diabetes, got a decent chunk of that done, and but have worrisomely little done on my synth paper on the total synthesis of pyranicin. Oh, and there's labwork to be done and so on and so forth...rawr. it'll be tough for the next few weeks.

But in more exciting news:
--there's a good chance that I'm going to Germany this summer to do biological chemistry work on a polyketide biosynthetic pathway.
--I may get to do a not-for-credit hang out in the lab and work on a project type independent study thing with my favorite prof (the one I worked for last summer who does the synthesis of OncoTools, or carboxyllic acids with pH switches to give them a pKa ~6.5 to target the acidic regions of small tumors that can be tagged with radioactive halogens...at least in concept...we haven't made enough of one to put it into practice, but yeah organic synthesis how I love thee).

Friday, November 21, 2008

I'm having a big dilemma over what courses I should take next semester. We are on a unit system (as opposed to a credit hours system), and a normal load is 4 units, although you can take 3.0-4.5 units without underloading or overloading.

Next semester I was originally signed up for:
--intro inorganic chemistry (1.0 units)
--statistical thermodynamics 1.0 units)
--metabolic biochemistry (0.5 units)
--biochemical methods (0.5 units)
--Johannes Sebastian Bach (1.0 units)

Bach is a musicology class to fulfill a distribution requirement with a professor I rather like, so it should be fun. This adds up to 4 units; a pretty normal schedule.

Well then I decided I didn't feel like taking i-chem lab. As a biochem major, it's not required. (I majoring in biochemistry & molecular biology, but at another school that had minors, I would probably be close to doing a minor in chemistry). In any case, I'm a little burnt out on lab classes. I love being in the lab doing research, but class labs are different. Everything isn't where you need it to be, they're short and hectic, and you can't do extended experiments because science doesn't work in once a week four block chunks. It's nice to be exposed to some lab techniques, but in reality I pick those up faster by doing research in a given field, and I'm kind of at a point where I understand generally how labs go and I'm not getting that much out of taking them anymore. Beyond biochem methods and analytical chemistry, both of which I need to graduate, I really don't intend on taking any more lab classes. Also next semester, then, will be the first time in college that I will only be taking one lab class (I'll probably still TA for organic, but whatever).

So the ramification of dropping inorganic lab is that I am taking 3.5 units. Still not technically an underload, but I started fishing around for half unit classes. This is dangerous, because in the sciences half units are classes that don't have lab components (it is pointed out frequently that all humanities classes meet with only a lecture component and you receive a full unit).

My first thought was a membrane-membrane interactions seminar. It's a 4oo level bio class where you meet for two hours a week to talk about molecular neuroscience papers. Seminars are pretty low key, generally, besides that one day when you have to stand up in front of ten or however many people are in the class and talk about a subject for an hour with our professor grilling you (and boy, does that prof know how to grill, he's a toughie). Otherwise, pretty mellow.

My second thought was advanced mechanistic organic chemistry. This might be a bit more work, but maybe not. It meets for three hours a week, and it's lecture only, so problem sets, articles to read. It's about MO theory in organic chemistry and it goes over the theory behind all those weird-ass concerted ring closings which would be nice to know about, even if my interests are ultimately more synthetically oriented (Woodward Hoffman rules, etc.) There's a lot of computer modelling. Also a small class, probably also mellow. With a number of my study buddies. It also may not be offered next year, whereas the biology seminar most definitely will.

My main fear is that if I take inorganic, advanced mechanistic organic, stat therm, metabolic, biochem methods, and a humanities class, I'm going to be drowning in work all the time even if it isn't technically an overload (I also might just maybe hate chemistry after taking all that at once...and will be taking no biology classes that semester). Especially since I am far from a p-chem-minded type and stat therm is going to be fucking hard for me. On the other hand I can always drop something (most likely advanced mechanistic or my humanities class) and I really shouldn't be afraid to do that. So, should I go for it, or is that crazy?

In other news, I am most likely going to doing labwork in Germany this summer in a chemical biology/biomolecular chemistry lab. More on that later.

Friday, November 14, 2008

I'm taking a topics in biochemistry seminar course where we read two papers a week. The topic the course covers this year is chemical biology.

Now, I'm someone who loves organic synthesis, who loves biochemistry, and who loves molecular biology. I think my mind is set up for the type of conceptual trouble shooting of organic chemistry on terms of diagrammatic reasoning as opposed to mathematical reasoning (like in a lot of computational and biophysical approaches). At the same time I'm an arrow pusher, and I think of this very much at a structural/chemical intuition level as opposed to a gross biological scale. But as much as I love organic chemistry I like applied organic chemistry. The entire complexity of biochemical systems is both fascinating and overwhelming. So where this rant is all going, is basically I thought chemical biology would be exactly my cup of tea.

Turns out that there are a lot of chemical biology projects that seem just sort of...pointless to me. Like they are doing an interdisciplinary project for the sake of being interdisciplinary? I'm skeptical, because a lot of these projects don't seem to be tackling interesting questions, really. I mean, there is some chemistry in there that appeals to me, some biology, but rarely do I find a paper where I think "yes, this is a good mix of concepts."

But I think, actually, I'm probably going to end up in a chemical biology program, it'll just be a matter of finding one of them that does something really cool, or the intellectual challenge of working on a piece of a collaborative project knowing the big picture but being an expert in a small area. Or somesuch.