The Boston ACS provided yet another opportunity to look at chemistry as a social networking phenomenon. Having attended several talks inside my areas of expertise (organic chemistry, medicinal chemistry, and chemical informatics), I was struck by two things:

1. Most talks were laser-focused on one tiny aspect of chemistry that is of little interest to the average chemist, but of great interest to a few chemists.

2. Those talks that were not as focused on details drew the biggest crowds.

These statements have nothing to do with the quality of the presentations. In fact, one of the best talks focused on the clinical trial data for a single molecule, the Type II diabetes treatment dapagliflozin (below). Although the members of the audience for this talk seemed interested as well, they represented only a tiny fraction of the ACS attendees.

Roald Hoffman's talk (and the symposium of which it was a part) drew a larger audience. Having won a Nobel Prize surely can't hurt. An association with recent controversy is also a plus. Of course, being a good story teller and genuinely likable also helps. On the other hand, I wonder what the turnout would have been like if instead of telling his scientific life story Hoffman had presented the details of a recent theoretical study.

The Boston ACS, and just about any analysis of printed chemical research reveals The Long Tail at every turn. Although usually applied to mass markets such as DVD rentals through Netflix, The Long Tail also provides valuable insights into scientific fields such as chemistry.

To use Long Tail terminology, Roald Hoffman and E.J. Corey are at the head of the curve - the blockbusters. They and their work are widely-recognized and discussed. Almost everyone else's work, regardless of how ground-breaking or clever, lies in the long tail of relatively obscurity. It is of great interest to a handful of people but essentially invisible to most chemists.

In a few ACS sessions, I counted as few as four or five audience members. The large number of ACS divisions and the astonishingly small audiences at some of their presentations are nothing more than a concrete demonstration of the Long Tail at work.

Each ACS division is a microcosm of the ACS itself, complete with it's own curve containing a few blockbusters (who are essentially unknown outside of the division) and everyone else in the Long Tail.

Not surprisingly, the collection and distribution of chemical information reflects the Long Tail character of chemistry itself. This simple but powerful principle has rather important consequences for chemists of all stripes, be they information consumers or information producers.

image credit: silver marquis

You can find them in nearly every scientific discipline: the anonymous science blog. For a variety of reasons, their authors have decided not to reveal their identities, as is their right. Styles range from the absolutely analytical to the cynically sarcastic.

I have nothing against anonymous science blogs. Some of the most interesting writing I've seen has been posted to them. But I do have some reasons why you might want to think twice before starting one.

1. If you're writing about anything remotely interesting, you will be identified sooner or later. Have you ever attended a scientific meeting and noticed how many perfect strangers you meet who know someone you know? Scientific disciplines are very small worlds. Not only that, but Google is a frighteningly powerful tool to find obscure information. If one of your colleagues stumbles onto your blog, chances are excellent they will be able to identify you if they're determined.

2. Owning your content keeps you sane. Have you ever noticed how otherwise considerate people can be very inconsiderate drivers? There's something about anonymity that brings out the worst in people. Connecting your name with what you write forces you to carefully consider what you're doing. And that's a good thing. You're going to be identified anyway (see above), so you might as well write like it from the start.

3. Consider your motive. What's the real reason you're writing under a pseudonym? Is it to be able to vent without consequence? To avoid upsetting your boss? Wanting to avoid colleague reactions or embarrassment? Uncertainty as to whether you're "allowed?" Do you worry about writing something that a future employer might not like, thus endangering you chances of getting a job? Going back to Point 1 above, you will be identified eventually. When that happens, will you be prepared to face the music?

4. Your current employer has rights. If you're working in industry, you've signed an agreement that gives your employer rights to your ideas and inventions. If you're in academics, your advisor probably doesn't want you disclosing the details of cutting-edge research. The immediacy and reach of blogging will turn scientific publication on its head; these are merely previews of the issues that lie ahead. When in doubt, ask before blogging.

5. It's a new form of scientific publication. Would you want to be an anonymous author on your scientific publications? Of course not. Every scientist is a businessperson, whether they like the idea or not. The business model is simple: trade your scientific reputation for money in the form of grants, salaries, bonuses, and job opportunities. Publication is the currency of scientific business. Blog-like scientific writing is simply its newest incarnation.

Own your content. The career you help (or save) may be your own.

image credit: flyzipper

You've heard the hype about PubChem, but you're still not convinced. In your mind, the fans have yet to show anything that PubChem does to make your job (which is to get stuff done in the lab) any easier. You've got SciFinder, which does everything you need to do. Why bother with this free Internet thing?

New technologies need to prove themselves. Those that don't simply disappear, or morph into something whose value is more apparent. With these thoughts in mind, here are five things chemists everywhere can use PubChem for right now.

1. Find the Structure of a Molecule by Name Ever wonder exactly what that drug company in the ad is trying to sell you? If you have the generic (or even brand) name, nine time out of ten, you can find the structure in a few seconds with PubChem. For example, here's the search result for the term "lunesta".

2. Look up a CAS Number Just about every reagent bottle has a CAS number on it. Sometimes they also have an IUPAC name that's difficult to parse. Maybe you've got a receipt with only CAS numbers and no IUPAC or trivial names. Plug that CAS number into PubChem and you're likely to get the structure quickly and conveniently.

3. Stop Drawing Molecules - Use a CID Instead Molecular structures are strange beasts. They can't be put into ordinary spreadsheet tables, don't travel well though email, and are a pain to draw in notebooks and reports. PubChem assigns all of its molecules a simple, short number called a Compound Identifier (CID). For example, the CID for lunesta is 969472. This CID does play well with email, spreadsheets, on Webpages, and anywhere else you might want to track chemical information. Because PubChem is a free service, you know you'll always be able to make the CID->structure conversion.

4. Browse and Search Supplier Catalogs With the recent announcement of Sigma-Aldrich's addition of 56,000 compounds, it's a safe bet that sooner or later, every supplier will upload their compound collection into PubChem. PubChem lets you search by supplier, or even limit your results to particular suppliers. This lets you conveniently search multiple suppliers from a single Web interface.

5. Link, That Ye May Be Found This one's a bit more out there. With PubChem's march toward becoming the world's compound registration system comes great possibilities. For example, every compound in the PubChem system can be accessed through a homepage. In the case of Lunesta, that page is here. Knowing that a Web page from another site links to PubChem's Lunesta page says some very important things about that site's contents, without much effort from the site's author. Following backlinks, as they're called, is the magic that enables services like Technorati and Google to makes sense of the Web. The next time you're blogging and refer to a compound, try linking to its PubChem page. You may find yourself listed at the top of a structure search without even trying.

A series of D-F articles have discussed InChIMatic, a Web application that lets you structure-search the Web using popular search engines such as Google. Recent articles have also described Firefly, a lightweight 2D structure editor designed especially for the Web.

Today, the first alpha release of Firefly is available for use with InChIMatic.

Despite its small size of only 103K, the Firefly applet offers a number of advanced features:

• A clean interface with major functionality in plain sight.

• Antialiased rendering. Pressing the "+" and "-" keys will zoom in and out to reveal rendering detail.

• User-overridable bond length and angle constraints. When dragging a bond, use Shift to relax both angle and length constraints, or Ctrl to relax only angle constraints.

• Automatic inside-outside double bond rendering.

• Built-in molfile import/export. Use the File->Import Molfile and File->Export Molfile options to copy/paste a molfile from your system clipboard.

• Automatic implicit hydrogen detection. The quadrant for hydrogen placement is chosen based on the bonds surrounding the atom.

• Twenty levels of undo/redo. The commands can either be issued from the menu, or Ctrl-Z/Ctrl-Y.

• Persistent molecule. When you visit another page and come back, Firefly remembers the molecule you were working on.

• No digital certificate authorization. Just start using it.

Firefly also incorporates a number of keyboard shortcuts to speed up structure drawing:

• 1-9 keys Builds a chain with the indicated number of carbons.

• a key Phenyl (aromatic) ring. When hovering over a bond, fuses the ring to the bond. When hovering over an atom, fuses the ring to that atom, if possible, or sprouts the ring.

• f, l, r, i keys The elements F, Cl, Br, and I, respectively.

• z and t keys The elements Si and Sn, respectively

• b, c, n, o, s, and p keys The elements B, C, N, O, S, and P, respectively.

• [delete] and [backspace] keys deletes whatever is underneath the cursor.

To use these shortcuts, simply hover the cursor over an atom and press the key on your keyboard.

Being an alpha release, this version of Firefly still has room for improvement. Your feedback is important. Please send questions, comments, and suggestions to the email address found under Firefly's "Help" menu.

Tobias Kind writes to say that a PubChem Power User Gateway (PUG) interface is now available for Java. The software, which currently consists of two Java source files, can be downloaded here.

image credit: angiemckaig