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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: Twitter: Dereklowe

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July 17, 2006

Pounding Sand

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Posted by Derek

My chemistry readership is used to thinking in terms of reaction mechanisms. Those of you outside the field who've gone as far as organic chemistry will have come across them, too: pushing electrons for fun and profit. Chemists really do think in those terms, I can tell you - it's not just something they torture the sophomores with.

Here's a page with some good examples of classic mechanisms. (Update: that link may not be able to handle the attention. Other mechanism pages can be found here and here, and there's a well-done Flash site here.) Non-chemists will note mainly the profusion of curved arrows curling around the page, and wonder what we must be getting out of that stuff. The idea, though, is that chemical reactions involve bonds between atoms breaking, forming, and rearranging, and those bonds are formed through electrons. So most of what goes on in organic chemistry can be thought of - very successfully - as the movement of electrons, and that's what the mechanisms are showing schematically.

But reaction mechanisms are also one of the things that chase people out of the field completely as students. The problem is, the lazy way to teach an organic chemistry course is as a Huge Heap of Reactions, to be memorized and tested on. Buy while there's no way around learning and understanding these things, teaching them as if they were species names in zoology is a crime.

There's an easier way, which more competent professors point out. The thing is, electrons don't just zip around randomly. They're negatively charged, so they prefer to go toward things with positive charges and away from other negatively charged ones. The various chemical elements can be more electron-withdrawing or electron-donating, so that means that any bond between two different ones is likely to be an unequal affair. The electrons are going to settle more on the end of the bond that's pulling on them, giving it a bit of a negative charge, and leaving the other end with a bit of a positive one. If you can keep track of full and partial charges, which isn't that hard, you're a long way toward solving any mechanism that a test can throw at you.

That page I linked to has some carbonyl (carbon-double-bond-oxygen) mechanisms, and I'm telling you the truth: the few things on that page are the foundation of umpteen dozen reaction mechanisms, which means that you have a choice when you're studying organic: you can memorize the whole shaggy list, or you can learn the fundamentals and apply them over and over in different combinations. Why anyone would do it the hard way escapes me.

But I've seen people take on a lot of tasks that way. When I was in high school, we still had to memorize and recite poems - not especially good ones, stuff like Longfellow's "The Builders" and the end of William Cullen Bryant's "Thanatopsis", poems fit to give Aaron Haspel the shakes, but poems nonetheless. (Good to see that he seems to be blogging again, by the way). And I recall one guy standing up to take on one of these set pieces, and as I listened to him slowly, haltingly stumble through it ("So. . .live. . .that. . .when-thy. . .summons. . . comes-to. . .join. . ."), my opinion of his skills evolved. At first, I thought that he was terrible at memorizing a poem. And, well, I still thought that when he finished, which was quite a while later. But what I came to realize was that he was a lot better than I was at memorizing a long string of random words, which is what he'd reduced "Thanatopsis" to. He went through all the commas, all the phrases like a snowplow. None of it meant anything; it just had to be shifted by brute force. And that's how he did it, and how some chemistry students do it still. It doesn't have to be that way.

Comments (19) + TrackBacks (0) | Category: General Scientific News


1. LNT on July 17, 2006 9:24 PM writes...

On a related note: What really gets me upset is when I hear about high school students forced to memorize the periodic table as part of thier chemistry class. What a waste of time and what a way to drive kids away from science...

(obviously, memorizing what the abbreviations stand for is important -- but thier exact location on the table along with the atomic #? For gods sake, THAT'S WHY WE HAVE THE TABLE - SO THAT WE DON'T HAVE TO MEMORIZE IT!)

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2. secret milkshake on July 17, 2006 11:31 PM writes...

A physicist I knew in Prague was fond of teasing us, the chem students, during his clases in quantum mechanics: "Not only the organic chemists know exactly where their electrons are located - they can even tell you where are these electrons going"

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3. Tot. Syn. on July 18, 2006 3:34 AM writes...

Sorry Derek, it seems that your vast readership, in a quest to the vahalla of cury-arrows, has killed the page you've linked to at Aberdeen University.

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4. Stuart on July 18, 2006 4:38 AM writes...

In my former life as a chemistry lecturer at UCLA, I would tell my students that all reaction mechanisms (the ones they would see in intro organic chem) were pretty much the same. I had quite a relaxed attitude to nomenclature as well - yes, you need to know the basics, but at a certain point it gets silly - some Profs would expect the kids to name a molecule that had three or four different functional groups with umpteen branches and perhaps a ring or two... what a waste of time. Once you get past a certain point in naming - one at which you are confident of them being able to communicate with each other and their teachers as well as understand exam questions - we call things molecule 3 or compound 27...

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5. Still Scared of Dinosaurs on July 18, 2006 4:42 AM writes...

Try this: "Excuse me, professor, but isn't this supposed to MEAN something?"

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6. John C. on July 18, 2006 8:25 AM writes...

Sadly, it wasn't until I was in grad school that someone finally sat me down and taught me the "figure out where the electrons want to go" system. I'd have had a much easier time in my undergrad if Prof. L. hadn't just insisted we memorize!

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7. Milo on July 18, 2006 10:18 AM writes...

I could not agree more with your comments. While I was a grad student, I had the pleasure of teaching an Org. Chem. course that was populated by mostly pre-med students. It was really sad to see how many of them did not do well for the simple reason that they tried to memorize and not understand.

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8. markm on July 18, 2006 10:53 AM writes...

I've never run into a college professor who didn't try to teach how everything fit together along with the items that must be memorized. Maybe that's an advantage of being a EE ratger than a chemist, or maybe I just made a good choice of university. However, from Kindergarten to 12 grade, I did have too many public school teachers who used the "just memorize the list" method. Every single one of them was too stupid and/or ignorant to understand how the subject they were attempting to teach fit together. One has to wonder about a college professor who uses the same approach...

LNT, I am no chemist, but I did have to take enough inorganic chemistry somewhere that I can still remember most of the periodic table 30-some years later. The way to teach that is to teach something about each of the elements, using the PT to put them in context. That is, pick a column and spend a few minutes on each element in it, from top to bottom. Physical properties, valence(s), reactivity, the kind of compounds it forms - and it becomes clear why the elements are grouped into those columns, and how various properties trend from light to heavy elements with the same valence. You don't just learn that Potassium goes into a particular box, but why it belongs in that box...

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9. Still Scared of Dinosaurs on July 18, 2006 12:17 PM writes...

Another way to teach the periodic table, which is complementary to markm's suggestion, is to convey a sense of the wonder that its existence used to evoke. Start with alchemists (ALWAYS start with alchemists) and talk about how much more sense the world made as the knowledge of the elements was built, and how each addition to the table opened new possibilities for doing stuff chemically.
You have to stop, however, just before the damn physicists ruined it all by breaking up atoms. Just fast forward to all the cool genes and proteins stuff.

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10. Lab Rat on July 18, 2006 12:40 PM writes...

They should come up with a something along the lines of what I learned to remember the first 3 rows of the periodic table:
"Happy Healthy Little Beggar Boys Catching Newts Or Fish, New Nature Magnifies All Sin P S Clarence Arrived"

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11. SRC on July 18, 2006 12:44 PM writes...

Teaching by rote memorization is reprehensible, IMO.

On the other hand, people who are over their heads in a field tend to memorize because they don't grasp the underlying framework, even when taught it. Those with more intrinsic ability recognize the common themes.

Learning the periodic table is to inorganic chemistry much like learning the names of functional groups is to organic chemistry. Can't have people talking about the reactivity of "C double bond O" groups. (Besides, most people already pretty much know the main group elements). It's unnecessary in high school, but pretty important in an upper division inorganic chemistry course, which discusses chemistry by comparing and contrasting members of a group. If you don't know which elements are in which group, you're stuck memorizing facts instead of grasping themes.

As for memorizing atomic numbers, see my comment above. One would hope that by the time one is an upper division college student one would realize that atomic numbers follow from the Aufbau principle, and so filling shells will take 2, 8, 18, and 32 electrons. Remembering the atomic number of a single element in the middle of the periodic table - say Mn, Z = 25 - means that Ru (one row down, one place over) has Z = 44. Easy. Memorizing such easily derived information is silly.

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12. sciwriter on July 18, 2006 7:29 PM writes...

i agree that the follow the electrons method is a much better way of having students think about organic chemistry. not only that, but by learning just a few types of reactions, tied in with following the electrons, students can learn how to see "the bigger picture"-- in other words, to have a few basic, solid tools that enable them to draw correlations and start to really think about how things work. i was taught this way, and felt it was invaluable when i got to grad school-- i found some of the rote memorization crew, despite their NSF fellowships, didn't always have such a deep foundation.

on the flip side, perhaps the subject GRE in chemistry needs to be rethought to incorporate more knowledge than memorization. my undergrad prof put little emphasis on nomenclature beyond the basics, and it worked to my disadvantage on the subject GREs (of course, it probably would hav helped if i woudln't have been so stubborn and would have agreed to study stuff i thought was useless...).

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13. eugene on July 18, 2006 8:35 PM writes...

You can teach students the underlying principle. But do they want to learn it? When they 'won't ever look at chemistry again when I'm in med school'. And are you going to catch up with all 200 of them to make sure they understand the mechanism and don't just memorize it and all the other reactions by rote?

Just because they answered a mechanism question right on a test, doesn't mean they didn't memorize it... Still, that's where adding a random methyl group comes into play.

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14. Still Scared of Dinosaurs on July 19, 2006 9:51 AM writes...

Per eugene's reference to pre-meds, the worst aspect of the teaching of organic chemistry where I was an undergrad was the assumption of responsibility on the part of the profs to uphold the rigor of the pre-med program. Rote may be an inefficient way to build organic chemists, but since it's harder and more work intensive it selects for the best students to apply to med schools. The fact that this has more to do with the fact that these are the same skills that correlate with high performance on the MCATs and not with actually being a good doctor is not apparently of much concern to the orgo profs.
This was glaringly different from most faculty at the school, which had the twin advantages of a good reputation and no graduate programs, which allowed the majority to put primary focus on actually teaching the subjects they had devoted so much time to learning.
In contrast, the chem dept once denied a popular prof tenure with criticisms that included the fact that she was "too approachable".

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15. Stuart on July 19, 2006 10:53 AM writes...

Students (pre-meds more often than not) would often complain that my o-chem exams were too difficult because the questions made them... wait for it... THINK. It's not necessarily fair to tar all pre-meds with the same brush, but there is a pre-med stereotype for a reason... Most of my students just wanted their 'A' at the end of the quarter, didn't care about why or how they got it, just wanted it. The fact that most of them wouldn't need to know what an SN2 reaction was a few years down the line is precisely why I tested them on their ability to think logically and solve problems - albeit in the context of o-chem. Try telling them that though... (as for the earlier comment about the random methyl group - you don't even have to be that extreme, just throw a deuterated reagent into a reaction where before they just saw the normal 1H version, that sorts out the students who just memorise from those who actually understand!)

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16. Elia Diodati on July 19, 2006 2:39 PM writes...

Pushing electrons is a nice concept when it works. But one should be aware of its limitations. Problems arise when you try to do the electron arrow dance on systems which are not well described by a single electronic state, for example transition metal complexes and photochemical reactions.

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17. clazy on July 19, 2006 3:33 PM writes...


The idea that your classmate memorized Thanatopsis as a string of unrelated words is wonderful. I'm sure you are correct that it was not a deliberate nihilistic protest against the poem's romanticism. I wonder though if the study habits of pre-meds is a nihilistic protest against organic chemistry?

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18. Still Scared of Dinosaurs on July 21, 2006 9:23 AM writes...

Problems with memorization of a string of unrelated words is one of the diagnostic criteria for ADHD, whereas understanding of underlying concepts and applying them ad hoc is one of the strengths of people with the same "disorder". Maybe we're all sharing too much.
Also, if you've ever spent time in a foundry you would know that pounding sand requires both strength and skill and can lead to amazing results when done well. You just gott have the right sand.

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19. delentye on July 23, 2006 5:58 PM writes...

That would've really come in handy for me a year ago, when I was taking orgo. And perhaps the other 100-odd of us who took the class, forgot everything, and developed such a distaste for the subject that we'll avoid mechanisms like the plague for the rest of our lives - despite most of us being in molecular biology.

Would you like to kindly put in a word in at the department for future Harvard undergrads' sanities, not to mention their wallets? (ie. We're paying to memorize this stuff?!)

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