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Confessions of a D Orbital

OleuropeinaOrganic chemistry has changed! Not the science, but the way it’s taught.

SUNY Stony Brook, Fall semester, 1973. 500+ wannabe doctors pack into the lecture hall, squinting as a small figure up front slaps down overheads, scribbling CHNOPS atoms and various dots and dashes, changing the acetate sheets faster than any human brain can register them. Each night after a lecture, like fatty acids emanating from the glycerol backbone of a triglyceride, we’d align in the library to copy the incomprehensible overheads at 3 Xerox machines.

Stony Brook University, Fall Semester, 2012. The professor, wearing a remote microphone and holding an iPad, walks about the cavernous lecture hall, as the students, in groups, work problems, helped by a troop of last year’s students. The entire event is available online for those who can’t make it to class.

Recently I received an e-mail from the new chairperson of chemistry at Stony Brook, Nicole Sampson, describing organic chemistry as “a bad memory for those pursuing the dream of entering a health profession.” I read on. “Fortunately, this situation has changed at Stony Brook. Professor Frank Fowler has been applying advances in the cognitive sciences, in combination with new technologies, to teach students how to take a complex set of data and use it to solve problems.”

So I e-mailed professor Fowler, who’d taught my husband’s organic lab. Larry, as a chem major, had small classes where professors actually talked to students. I was among the great horde of pre-meds.

“Sure, I’d love to talk to anyone who’ll listen. The old days were not the good days,” Fowler answered to my first e-mail.

If it weren’t for organic chemistry, I’d be an MD.

I knew by the first chemistry test freshman year 1972 that my childhood dream of becoming a doctor was over. By the end of my third semester of chemistry – the first of organic – I’d earned my third “D,” and was henceforth known as the D orbital. (By a statistical fluke, I got a C for the fourth semester. It happens.) I did, however, earn A’s in the lab, so I was not a complete moron.

I hadn’t yet taken biochemistry, so didn’t think anything that flew past in organic was of any relevance to medicine. At the risk of inducing an anxiety attack, I just unearthed Morrison and Boyd, the classic textbook (who knew I’d grow up to write those things myself?), to see if I’d have a flashback. And I did.

I looked up Friedel-Crafts alkylation, a phrase hovering in my distant memory, and soon discovered that this is the addition of a carbon-containing group to a benzene ring. According to the textbook, “In Friedel-Crafts alkylation, the electrophile is typically a carbonium ion. It, too, is formed in an acid-base equilibrium, this time in the Lewis sense,” followed by several reactions.

“What has this to do with setting a bone, removing a spleen, delivering a baby, or treating cancer?” I bellowed to my husband.

“The human body is a giant chemistry set that’s making and breaking covalent bonds,” he answered, obviously brainwashed. So I asked the same of the good Dr. Fowler.

“If anything, a molecular knowledge is more important for physicians and people going into health care now than it ever was. My dermatologist said, ‘I never use organic!’ But skin cancer is a perfect example of photochemistry of the skin,” Fowler said.

“So what’s changed?” I asked Fowler on the phone.

“We understand better how students learn, and it’s not when you talk at them. They learn by doing.”

The 1100 students in his two classes use the “inverted classroom” paradigm that is sweeping education and is working well in teaching genetics – students learn the material on their own time (hence delaying the extinction of textbook authors like me), then work in groups to solve problems during class.

“Work in groups? In organic?” I blurted, astonished.

“A group without a lot of smart people can get the right answer more frequently than just a smart person. This is very important in solving problems in the future,” Fowler said, insisting that today’s students are different. They eagerly work together, free of the anger and competitive streak that pervaded my own class, when everyone did anything to get the highest grades possible, lest they fail at the lofty goal of getting into med school. I even saw one student, whose name I still remember, spit into someone’s flask in lab, to better his own grade.

But I don’t think even a group of Einsteins could have helped me, because I just couldn’t see molecules in three dimensions. It’s inborn. Today, I can’t follow a dance instructor who faces the class – my brain can’t flip the perspective.

gleevecI thought that being able to rotate molecules on a laptop would have helped me, seeing the active site come into view as its substrate approaches, like this molecule of the drug Gleevec nestling into its target kinase (subject of next week’s blog). But Dr. Fowler still relies on handheld, tinker-toy like molecular models. “Life is 3D. You won’t understand problems in medicine if you don’t understand that a lot of molecules look alike because of their shape.”

He timidly brings up the gender factor. Do boy toys, like tools and model kits, better prepare kids to see molecular interactions in three dimensions, compared to Barbies? I think it’s a case-by-case thing. I grew up with model kits and war toys, and all I ever did with dolls was rip their heads off.

I might have benefited from Powerpoint presentations, though, which bridge the overheads of my time with modern animations too fluid to follow. “With Powerpoint you only see stuff come in and disappear. You can take a single topic, maybe 8 slides worth, and no student can tell when I go from one to the next. I can tell a much smoother story,“ Dr. Fowler says. He also uses “clickers” so that students can provide real-time feedback  on whether or not a concept is penetrating.


stethoscopeThe day after I spoke with Dr. Fowler, a Perspective by David Muller, from Mt. Sinai ‘s Icahn School of Medicine, appeared in the New England Journal of Medicine, describing a new way to prepare students for medical school that absolves them from much of the misery of organic chemistry.

The pre-med mantra of science courses, Muller wrote, was “used to cull the herd of talented aspiring physicians.” Sociologist Donald A. Barr from Stanford University and colleagues from there and UC Berkeley also point out in “Chemistry courses as the turning point for premedical students” that students from under-represented minority groups have a particularly difficult time staying on the path to a career in medicine, a problem largely attributed to chemistry courses.

Since 1987, Mount Sinai has encouraged humanities majors to apply to the medical school. Those accepted can learn “clinically relevant” parts of organic chemistry and physics in an 8-week summer session, and no Medical College Admissions Test, the MCAT. The Humanities and Medicine Program (HuMed) did so well in preparing future doctors that it’s evolved into FlexMed, which encourages students of all majors to pursue medicine at Mt. Sinai.

Half of each new medical school class at Mt. Sinai will consist of these more broadly-trained individuals. The school will recruit students as sophomores and “assure” them of acceptance by summer, junior year. As undergrads they’ll take two semesters each of biology, chemistry, any science lab, and one semester of physics, statistics, ethics, and health policy (or global health or public health). Proficiency in Spanish or Mandarin is strongly encouraged.

A person can now become a physician yet avoid the year of organic chemistry with lab. Ditto the MCAT. (My favorite sentence about reliance on MCAT scores: they “effectively exclude bright, creative, motivated students who aren’t strong test takers.” Me.) But I imagine selection will be challenging. “We will use many of the same metrics we use in our other selection models: evidence of excellence in research, community service, clinical exposure, athletics or the arts, clinical experiences, evidence of leadership ability, etc. We will also look to grades and SAT or ACT scores for some general sense of academic competence, but they won’t be the deciding factor,” Dr. Muller wrote in an e-mail.

If I weren’t out to pasture since being culled from the herd, I’d sign up.

Organically-grown, soon shortened to simply organic, foods became popular shortly after my traumatic encounter with organic chemistry. At first I wondered how a food could NOT be organic, NOT contain carbon. But of course the designation refers to freedom from pesticides, as if manure doesn’t contain carbon.

According to the dictionary, “organic” means “derived from living matter” or
“compounds containing carbon.” But the meaning has morphed into “natural,” “good,” or “better than that chemical-drenched crap.” The word that still gives me palpitations and makes me think of ketones and aldehydes has come to be nearly synonymous with “healthy,” and people will readily pay three times what the regular stuff costs, for that illusion of superiority.

Researchers at Cornell University’s Food and Brand Lab recently described a “health halo effect” that refers to consumers’ perception of superior taste, appearance, fewer calories, and overall value to any food bearing the flag “organic.” They asked 115 folks in an Ithaca, NY mall  to compare organic versus regular versions of yogurt, cookies, and potato chips. The pairs were, of course, identical, the perceptions not. Anything labeled organic was deemed healthier, tastier, and even less caloric. Perhaps the investigators should have compared, say, carrots instead of prepared foods.

Krebs shirtI survived my three D’s in organic chemistry. Occasionally I still have a nightmare of being in that lecture hall, trying and failing to fathom anything, re-living the desperation of knowing my score on an exam would equal the number of answers I got right by chance. My husband has helped by taking the same approach as allergy treatments, desensitizing me with a tee-shirt bearing the citric acid cycle. In the end, I found the clear logic of the relationship among three types of molecules much more comforting than the mysterious named reactions of organic chemistry: DNA, RNA, and protein.

  1. An organic chemistry related blog post should not be titled with “d-orbitals.” This is because d-orbitals are most relevant to transition metals, which are the subject of an inorganic chemistry course, not an organic chemistry course. The elements used in organic chemistry are too light to even have d-orbitals.

    Secondly, I don’t believe that seeing molecules in three dimensions is really necessary to succeed in a regular level organic chemistry course, mainly because I did well in organic chemistry and I can’t see molecules in 3D (though the ability to see molecules in 3D certainly helps). The carbonyl and aromatic reactions don’t require 3D visualization because carbonyl groups and aromatic rings are planar (e.g. Friedel Crafts reactions are aromatic ring chemistry). The Sn2 type reactions require the knowledge that the tetrahedral carbon atom flips its conformation, but that’s about it. To understand steric hinderance, it does not take 3D visualization to realize that the tert-butyl group results in more steric hinderance than a methyl group.

    The figure that you showed in your post is of a protein, and I have found that protein chemistry really isn’t covered all that much in organic chemistry classes, at least not to the extent that you need to visualize the protein in space. Something like that probably isn’t covered until some sort of structural biology class, and even then, they probably have computer modeling for things like that.

    In my mind, the most important things to understand with organic chemistry are acid/base reactions and electronegativity.

    Third, I actually agree that it doesn’t really make sense that organic chemistry is such an important prerequisite for medical education. Frankly I couldn’t care less whether the surgeon who operated to remove my appendix knows whether nitrobenzene is more or less reactive than toluene in a Friedel-Crafts reaction. (P.S. Nitrobenzene is less reactive).

    I liked your segment on organic food. When someone says organic food, all I can think about is eating some white powder that smells of dimethyl sulfoxide residue. Actually, the reality is not much better. Organic food takes provides less yield per acre, so less food can be grown on a piece of land. As such, it is more difficult to make less food to feed everyone on the planet, and poor people in third world countries are more likely to suffer from famine.

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