The Walking Dead? Organic Chemistry Lectures Online

AMC’s The Walking Dead is one of my favorite shows on television these days. On top of excellent acting and a compelling storyline, the show is legendary for its special effects, which hold nothing back in terms of violence and gore. Zombies have taken over the world, and the show follows a small group of human survivors as they cling to life in and around Atlanta. How exactly did a bunch of mindless, flesh-eating, slow-walking undead best the United States military, Interpol, nuclear bombs, etc.? Good question…

Here’s a (somewhat) related question, about a situation just as ugly: how could a subject as compelling as organic chemistry be given as dull a treatment as those currently available on iTunes U? The linked lectures are by J. Michael McBride at Yale, and are (long story short) the “best” organic chemistry lectures available on that platform. The problem? They’re a poster child of God-awful teaching. Where do I even begin…?

More compelling: The Walking Dead or organic chemistry lectures online?

More compelling: zombies from The Walking Dead or organic chemistry lectures online?

Let me start by calmly stating that I have no problem with the content that McBride covers, per se. His content is fine, and cuts a nice swath across a variety of topics. If the student buys in, she’ll leave McBride’s course with a solid awareness of important results and thought processes in many areas of organic chemistry. What he teaches is largely irrelevant, but I take enormous issue with how he teaches.

I probably don’t have to tell this audience that good teaching should reflect how people learn, not how a discipline is structured—or even how knowledge is structured in a professor’s mind. Good teaching must include live practice and feedback, right at the moment of learning, in the classroom. Good teaching must feature concrete, attainable learning goals. Good teaching should be a conversation, not an oration. If it must be an oration, the structure of good teaching should invite the student to consider a problem or challenge her current worldview. McBride’s lectures—and most other organic chemistry lectures I’ve seen online—do none of this. He assumes, erroneously, that his responsibility is simply to say words in class. Even so, his words don’t challenge, confront, or question…his videos are as good as Reusch’s Virtual Textbook of Organic Chemistry (which, by the way, is a phenomenal resource). One might argue that the videos are even worse than text, insofar as they aren’t searchable and may be a waste of the student’s time. In spite of its flaws, Khan’s organic chemistry series does a better job of presenting compelling problems and asking the student to consider them than McBride’s series. That the community of organic chemical educators would relegate good teaching to the likes of Salman Khan is downright embarrassing. That McBride actually taught in a live classroom at Yale is also disheartening!

MOOCs have captured the world’s attention in recent months, which means that online educational content is seeing more scrutiny lately than it usually gets. Some educators have been optimistic about the situation, others cynical. Me? I’m still on the fence, but I welcome the opportunity to have my teaching put under the microscope. In spite of what Bill Gates says, chemistry content online is not what it should be, and pales in comparison to comparable content in…political philosophy, let’s say. Reusch’s VTOC has entered its teen years with no comparable interactive replacement. Opportunities to practice organic chemistry and learn interactively are very few and far between right now. Our situation is frustrating, but inspiring to the extent that we have a lot of room to grow.

Perhaps I’m over-reacting…I have a tendency to do that. Still, I would rather be chemical education’s harshest critic than hear the same legitimate criticisms from outside the field. Would love to hear your thoughts about chemical education’s relation to the MOOC craze, and how you think we’re doing. Thanks for reading!

Chemoinformatics Curiosities: A Chemical Educator’s Perspective on InChI

Organizations supporting machine-readable molecular formats.

Organizations supporting machine-readable molecular formats.

When it comes to machine-readable representations of molecules, I grew up with SMILES. A SMILES string reflects the connectivity and stereochemistry of a molecular structure, and may be generated from any number of other machine-readable formats, such as MOL and CML. SMILES strings are becoming ubiquitous on the web, thanks to giants like Wikipedia. They’re nice because they’re fairly short and readable—the SMILES string for ethane is simply “CC,” for example.

That said, the limitations of SMILES are difficult to ignore. The same readability that makes SMILES appealing to human eyes limits its scope significantly. The innards of the SMILES algorithm(s) are fairly simple from a chemist’s perspective, and do not take into account spontaneous structural changes like tautomerization (or even the structural equivalence of resonance forms). There are multiple algorithms, meaning there is not, strictly speaking, a one-to-one relationship between structure and SMILES string. Finally, SMILES is a proprietary format whose algorithms are kept under lock and key—with the notable exception of the OpenSMILES project.

IUPAC, chemistry’s own group of nerds with a nomenclature fetish, has been working to remedy this situation for over a decade. Their machine-readable format, the International Chemical Identifier or “InChI” (en-chee), reflects a completely different philosophy from the SMILES approach. The goal of InChI is not to fully represent molecular structure, but to generate a unique identifier for a particular compound, given a structural representation. The InChI folks recognized that molecules can be represented with varying levels of detail, and that we may not necessarily need all the details to uniquely identify a particular compound. Many species, for example, can be singled out by their molecular formulas and connectivity alone. H2 is a nice example—to uniquely identify H2, all we really need is its molecular formula and knowledge that the H’s are bound together. More complex compounds, such as those that may possess stereoisomers, need more details in their identifier. Continue reading →

Organic Chemistry on the Web 2.0: the OrganoWiki

When it comes to organic chemistry on the web, for substances, there are a variety of useful resources. ChemSpider, Chempedia, and even SciFinder are wonderful for discovering the known behavior of chemical substances. Sadly though, the same cannot be said for chemical reactions, the (arguably) forgotten branch of organic chemistry on the web. While established websites like organic-chemistry.org provide a great deal of information on a variety of organic reactions, their visibility and attractiveness to newcomers to the field (including students) are significant disadvantages. Improving the quality and web presence of organic reactions on the web is still very much an open problem.

When I began working with the editorial board of Organic Reactions to produce condensed versions of OR chapters for use on the web, the question that burned in my mind was: what is the best way to maintain OR‘s authority as a secondary reference work on the Internet, given the desire of web users to engage directly with (read: edit) web content? The answer, I believe, comes in a sort of two-tiered system—literally juxtaposing user-generated content and content from the “experts.” After all, synthesizing knowledge from a variety of primary sources is the goal of any secondary reference work…and in today’s Web 2.0 age, there is no reason why coverage of a topic has to end at the publishing of a review, or with the search efforts of a single individual author. Why not let user-generated content (recent reports from the primary literature, experimental “know-how,” etc.) keep an expert’s review on the cutting edge?

That’s the philosophy behind the OrganoWiki, a new website launched by Organic Reactions in the fall of 2010. Check it out! After registering for an account, you’ll be able to edit the Discussion pages associated with each article. The articles cover organic chemical reactions and are based on Organic Reactions chapters. Some of my personal favorites:

[3+2] Nitrone-olefin Cycloaddition
Phenol Oxidation with Hypervalent Iodine Reagents
Reductions with Hydrosilanes