This is dumb

I was reading a paper today, and it indicated in its figure legend that it used CS ChemOffice to draw some organic structures. And I begin to wonder, why the fuck is this information necessary to include in a figure heading?

I mean, I get with proteins and shit that it's important to say what program you used for your refinements and such when presenting a structure because...uh...that's part of your method. But this a) was not presenting novel results--just giving background in the intro and b) is there really any substantial difference between a line drawing made in ChemDraw versus a line drawing made in IsisDraw/BKDraw/ChemSketch/whatever? Why don't we say "I did my word processing in Microsoft Word." Or "I analyzed my data in Microsoft Excel." "I did my lit searches in PubMed." Or "I looked up this reaction on SciFinder". Or "I edited my gel images in Adobe Photoshop". Yeah, I guess you get the picture. I just don't understand why this is in a JBC article.

On Review-Writing

About a month ago, my PI asked me if I'd like to write a minireview with him. This was like "whoa seriously?", and I dove into a huge pile of papers on primarily pretty obscure natural products research. This is really only an opportunity afforded to me because a) my PI is a really nice guy and b) I'm an American abroad, so being a native English speaker is considered a huge advantage and c) I have no idea, it just sort of happened when I was in his office one day. I've been slogging through a ton random plant pathways in old articles from the '70s and '80s in Phytochemistry and huge exhaustive Angewantde reviews on polyketide biosynthesis and biosynthetic Diels-Alder reactions and Natural Products Reports reviews on biomimetic synthesis and so on and so forth.

I'm kind of known in my lab for being strangely obsessed with reading papers for a 21 year old student who isn't done with her bachelors yet. I don't know when I got into this habit, I guess over the past year or so I realized that reading papers on my Google Reader RSS feeds was a great way to procrastinate memorizing point groups and doing arduously long problems on the Boltzman Speed distribution when I just wasn't in the mood for it. It's also a habit, I guess, that people encourage in me, like attending seminars, so it tends to get reinforced. I am lucky enough to attend an undergraduate institution that puts a lot of emphasis on processing the primiary literature, so in a sense doing a minireview is just a step up from writing a review-style term paper, which I have written several of. It needs to be more polished and incorperate more references, but in essence the task is the same: read a shitfuckton of papers, summarize them, re-draw a bunch of schemes in ChemDraw the way you want them drawn to illustrate your point, and keep reworking the document until you're like "when the fuck will this goddamn thing be written?" while somehow perversely enjoying the process.

So, I have a first draft written, and thus I've stepped into the process of starting to seriously write it instead of it just being some abstract Thing. It's just I talked to my PI last week and he was like "oh yeah, well I think we should re-order the examples like this and this and this and by the way this random metabolite pathway actually incorperates this intermediate not the one you have drawn and here's 8 million more references because I think you should talk about xyz pathways as well. But I don't want it to be exhaustive! Oh, also, you should download the paper template to the journal I want to submit it to, even though we are far from done writing it." I'm a little bit overwhelmed by the prospect of re-ordering all the ideas and putting them in a cohensive whole because, well, god, I don't know, it just really is a lot of work that still needs to be done. Also, I fucking hate when you track down eight references from some obscure research done in the '80s only to find that there was a relatively recent review article that incorporates much more recent findings on the topic that for whatever reason just wouldn't show up in your original Web of Science search. You find out in review writing that there's a lot of trash published in the literature, like structures that are just plain wrong or have ambiguous stereochemistry when they really shouldn't (endo or exo isomers in Diels-Alder reactions are, uh, kind of important, and you'd think something that one could elucidate via NMR) and a lot of citations that are just wrong (like papers that were published in 1982 cited as being published in 1992? and when you can't track down the reference you're like...wtf is wrong with me? oh wait. no, it's not me, it's them). I guess I also have my fair share of problems with making stupid chemical errors in my schemes and reference list, though, so I shouldn't be so harsh.

Also, I seem to have some paper that for the life of me I can't figure out what it has to do with the topic I'm writing about. I'm pretty sure it's a paper he handed me and not one I found on my own. It's like "blah blah blah his tag blah blah blah PCR blah blah blah protein expression blah blah blah enzyme blah blah blah iron center blah blah blah".

But yeah, it's a process. An interesting one, at the very least.

RSS feeds

So instead of doing anything productive today, like studying for/finishing my midterms, I decided to add several journals to my google reader in hopes that RSS feeds will provide me with more procrastination opportunities inspire me to keep up with the lit. The problem means diverse interests=lots of journals I could (attempt to sort of) keep up with. Right now I have RSS feeds for Nature, Science, JACS, JOC, JBC, JMB, PNAS, Journal of Med. Chem., Angewandte Chemie, Biochemistry, Bioorganic Chemistry and Organic Letters. Which is pretty much everything on my list except Cell, Tetrahedron, and Synthesis, which I can't find an RSS feed for on google reader. Oh I guess I could add Chemistry & Biology and a few more, but anyway this list is getting unmanageable. I was surprised to not find Cell, but it seems that synthetic chemists are bigger RSS feed users than biologists because I found more obscure chemistry journals than obscure biology journals with feeds set up.

Regardless, we'll see if I actually skim through the lit now, or if it just piles up as more unread stuff on my google reader.