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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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July 19, 2005

Sitting Through Some Chemistry

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Posted by Derek

Physics prof Chad Orzel published a guide last week to surviving organic chemistry seminars. (I can understand that that's a particularly high priority for people who don't know any organic chemistry and have to sit through these things, actually.) He provides what is, for an organic chemist like me, an interesting man-from-Mars viewpoint:

"Stage Two: "Here's the stuff we start with." This will include a couple of diagrams showing different arrangements of hexagons. The jargon will get pretty thick, here, but almost all the strange words will be names of different parts and sub-parts of molecules. . .

Stage Three: "Here are the steps in the process." This will include at least one slide showing multiple diagrams of hexagons, with arrows between them. The jargon will again be pretty thick, but here, all the strange words will refer to methods of sticking pieces of molecules together. . ."

Ah, but are these the hexagons with little circles in the middle of them, or the plain ones? Very different, those guys are. Since he didn't mention dashed and wedged bonds, I'll assume it's the former. Rarely will those arrows point from one kind to the other, by the way. You can turn the circle-inside guys to the uncircled kind and vice versa, but it takes some real hammer-and-tongs reactions to do it. I haven't run one of those for over twenty years now, to give you the idea.

Keep in mind that we use pentagons and heptagons, too, but you won't see many circles inside them (although it's possible, especially if you're sitting through an organometallic chemistry talk.) Squares are rare, but triangles can represent a group that I've always liked, and that I have a reputation for introducing into my lab's molecules.

Once you've staggered through the talk, there's the problem of questions at the end, naturally. Orzel's advice:

"If you absolutely need to ask a question, remember that the crucial figure of merit for these talks is the "yield," which basically means "How much product do you get for a given volume of reactant?" If the speaker hasn't mentioned the yield specifically, you can't go wrong asking "What's the yield like?"

If they have stated the yield, ask "How does the yield stack up against other methods of producing this stuff?"

If they have stated the yield, and compared it to existing methods, and you still feel a need to ask a question, ask about the solvent peaks/ blobs/ pencil marks.

Questions of the form "Why are you trying to make this stuff in the first place?" are usually considered unsporting. . ."

Ay, that's for sure. I'm glad no one asked me that last one during my PhD defense, because by that time I'd begun to realize that most of my possible answers were pretty weak. I sure don't think I'd have been able to get them out with the tone of conviction I'd have had three years before. As I told people near the end - no, not my examining committee, what do you take me for - "The world doesn't need another synthesis of this molecule. But I do."

But I'd ask Chad to take heart - I don't hear many physics presentations, but I do have to sit through some pretty gritty molecular biology talks from time to time. I can deal with those, for the most part, except (as I've mentioned) for the sneaking suspicion that I've been seeing the same electrophoresis gel since 1987.

And, frankly, I'm not all that good at sitting through talks in my own field. My tolerance of uninteresting work has not improved over the years, and my definition of "uninteresting work" is gradually becoming more inclusive. It's to the point that some of my colleagues give me the raised eyebrow when I actually show up at a seminar. I feel, in other words, Chad's pain.

Comments (11) + TrackBacks (0) | Category: The Scientific Literature


COMMENTS

1. jeet on July 20, 2005 11:57 AM writes...

What? I don't get it. The molecular bio stuff is the greatest.


OK, that may just be me.


If you are suspect of the 2-D data, make sure to ask if they have run the bands in the mass spec.

Permalink to Comment

2. jsinger on July 20, 2005 12:20 PM writes...

Having been required to take a year of organic chemistry lab to become a molecular biologist, a requirement that has not benefited my real-world work one iota (although it was really fun), I always enjoy the rare organic chem seminar. It's always a kick to see those vaguely familiar terms, methods and devices -- it's like when I catch an old Miami Vice episode on TV.

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3. Derek Lowe on July 20, 2005 2:22 PM writes...

Some seminars outside my field, though, are like watching Miami Vice in another language. I recall seeing reruns on German TV during my post-doc: "Was is heir los, Crockett?" "Keine Ahnung, Tubbs."


Mind you, in my experience, that was very close to the most entertaining thing on German TV at the time.

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4. Linkmeister on July 20, 2005 5:05 PM writes...

Gee, Derek, you should have done your post-doc in Japan. When I was there (1972-1974 doing Navy service, not scientific) Japanese TV was all anime and early manga, and none of it was subtitled.

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5. qetzal on July 20, 2005 5:24 PM writes...

Well, since we're veering off topic a bit -

First time I went to Germany, I watched a sports program on TV that I still can't quite believe was real.

Picture indoor soccer played by two-man teams riding bicycles, and they're only allowed to hit the ball with parts of the bike.

They were amazingly good at it. They'd do a 'wheelie' and snap the handlebars to hit the ball with the front tire, or go up on the front wheel and swing the whole bike frame around to hit the ball really hard with the back wheel. Oddly like wrist shots and slapshots in hockey.

As far as I could tell, there was some kind of actual league with teams from different countries competing.

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6. The Novice Chemist on July 20, 2005 6:21 PM writes...

As a grad student, I have to go to mandatory seminars from other divisions in chemistry. Sometimes, I have an index to measure how fast it will take me to lose focus or fall asleep. If there's mathematical equations in the first three slides, I'm definitely losing attention. More than one simulation or crystal structure usually gets me, too. I'd definitely rather watch Miami Vice in Farsi.

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7. daen on July 20, 2005 6:28 PM writes...

There's a 50:50 mix of molecular biologists and organic synthetic chemists in our company. Our technology requires ligating oligonucleotides and linking together small molecular fragment building blocks, all in the same pot. The possibilities for disaster are many. The discussions revolving around possible solutions to the problems can be ... refreshing. Understandably, neither chemists nor biologists who have spent weeks fine tuning their parts of the protocol are especially keen to go back a few squares on the snakes and ladders board.

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8. daen on July 20, 2005 7:21 PM writes...

Incidentally, when I was working in Berlin, it used to given me enormous pleasure to watch "Star Trek: Raumschiff Enterprise" ... after a few weissbiers, of course, to help get my Babelfish working. "Beamen sie uns hoch Mr. Scott". Rather, "Auf wiedersehen, Mr. Scott".

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9. Peter Ellis on July 21, 2005 4:04 AM writes...

As far as mangled language goes, I've seen Star Wars Ep. IV dubbed into Malay, with Chinese and English subtitles.

Amusingly, the English seemed to have been generated by retranslation from the Malay

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10. Brian on July 21, 2005 5:37 PM writes...

The greatest invention since electrophoresis in molecular biology has been adobe photoshop. You probably are seeing the same gel from 1987, just with a few touch-ups. Got a band that's not supposed to be there, a little cropping or contrast adjustment and viola - its gone!

Permalink to Comment

11. chuck on July 22, 2005 10:32 PM writes...

"And, frankly, I'm not all that good at sitting through talks in my own field. My tolerance of uninteresting work has not improved over the years, and my definition of 'uninteresting work' is gradually becoming more inclusive."


Meeeee tooooo!!!!! I am sooo *over it*. How much money does it cost my company to be sitting bored in a room listening to a dull talk? Do our shareholders know about this? I wonder.

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