A quiet revolution is taking place in the way the primary research literature gets reviewed. Like all revolutions in their infancy, this one looks hungry, raggedy and generally not respectable. But that could change rather quickly given the right technology.

Research Blogging is a brand new service that aggregates commentary about the peer-reviewed literature appearing on blogs.

Let's say Mary the Chemist finds a procedure in a paper on reductive amination that solves a problem she's been having in isolating her products. After having used the procedure awhile, she notices that one class of substrate not described in the original paper gives much lower yields than those reported. Not having the resources to create a complete paper around her observation, she decides to write about what she found and post it to her blog.

If that were the end of the story, it's very unlikely Mary's posting would be of much use. Although Mary's blog is read by a couple of hundred people daily, few of the readers on the day her posting appeared had an interest in reductive amination or the paper she discussed. And none of her readers on that day were able to follow up on her observation.

Mary continues to post to her blog and eventually her observation, of potentially great value to the right chemist, gets buried in the archives (and on page 3 or 4 of most Google searches).

Enter Research Blogging, a Web-based database associating blog entries with references to the peer-reviewed scientific literature. Some time before writing about her observations, Mary signed up for a Research Blogging account and registered her blog with the service. At the time she wrote her observations on the reductive amination reaction, Mary applied special markup to the posting to make it readable by Research Blogging's automated system.

Instead of disappearing into the digital abyss, Mary's observation becomes permanently associated with the original paper.

Although Research Blogging's user interface is currently primitive, it's unlikely to remain so for long. The founders of the service appear both motivated and committed, recently forming a non-profit corporation to support their work.

In the future it's not inconceivable that Barry the Chemist, after having finished doing his CAS search on reductive amination methods would next turn to Research Blogging to make sure he really knows everything written about the three most promising peer-reviewed papers he's considering using.

Research Blogging is a wonderful idea with great potential to fill a significant need. Like any new technology, though, there are some issues to work out. The next article in this series will offer some ideas.

A recent D-F article discussed the potential for online videos in chemical research. Although chemistry has been slow to catch on, biologists have been busy creating phenomenal video content. One of the best efforts in this space is the Journal of Visualized Experiements (JoVE).

YouTube videos spread so quickly in part because of their ability to be embedded into other Websites. This might not seem like a big deal, but it is. The reason is simple: when you embed someone else's content in your own, you create something fundamentally new.

Although JoVE doesn't yet support public video embedding, it's a feature under active development. Nikita Bernstein, co-founder and editor of JoVE, was kind enough to provide me with an early preview of JoVE video embedding. You see the result displayed at the top of this article. Videos can be embedded both in a vertical format, as is done here, or a horizontal format.

Now, if you're a chemists, injecting mosquitoes may not be your thing. But just think about all of the procedures you've done that used an unfamiliar apparatus, produced an unusual color, called for a difficult crystallization, foamed, became too viscous to stir or filter, or used an uncommon technique. Think of all of the details essential to reproducibility that get left out of a written description. Then think of all of the dirty jobs that are carried on by oral tradition: maintaining a dry box; dealing with flammable spent catalyst; cleaning a solvent still; quenching butyllithium.

Video certainly won't be useful in documenting every part of chemistry, but there are vast swaths of unexplored territory, such as experimentals, where it could change the game significantly.

Depth-First began with a single post on August 12th, 2006. One year and 193 posts later, I thought it would be interesting to reflect back on how my expectations about blogging diverged from reality. Many of my observations come from statistics compiled by Google Analytics. An investment in time to install and use analytics software more than pays for itself within a few weeks.

With these thoughts in mind, here are ten things that surprised me:

1. The Undiscovered Continent of "Gray Literature." Like television networks, scientific journals serve subscribers with often wildly differing interests from yours. Some content will simply never make it into a print journal, no matter how useful or newsworthy. When you publish a blog, the only OK you need is your own. This means you can tackle subjects that are literally impossible for scientific journals to cover. In fact, your blog can contain valuable content not available anywhere else. After you wrap your brain around this simple concept, the most interesting things can start to happen.

2. It takes about six months of constant writing to see signs of being noticed. This is the phase during which I suspect many bloggers throw in the towel. Unless you already enjoy world renown in your field (in which case you're probably not blogging), expect to pay your six month dues.

3. Syndication matters. A lot. When I started D-F, I couldn't understand why people seemed so excited about "syndication." But I did notice a steady build-up of traffic on my server logs dedicated solely to accessing my RSS and Atom feeds. I decided to track this traffic using FeedBurner and discovered, to my amazement, that it accounted for about a third of all non-robot traffic on my site.

4. Readers take the weekend off. Traffic drops off rather significantly (50-60%) on weekends. Conversely, traffic peaks quite consistently on Wednesdays. Although the former is understandable, the latter continues to puzzle me.

5. For niche subjects, AdSense sucks. Chemistry is a subject dominated by niches. Any recent ACS program will show 40+ divisions; chemistry is all about the long tail. In the early days of D-F, I experimented with AdSense and got nada. This made sense (pun intended) because the ads being shown had almost nothing to do with what I was writing about. Adwords can work very well for broadly-appealing subjects. But if you're writing about your area of scientific expertise, which by definition is about as niche as you can get, AdSense is more likely to be an eyesore than a source of income.

6. Your most valuable asset: the archive. On a typical day, only about 15% of D-F's pageviews come from a user landing on the homepage itself. The rest come from pages previously found and linked to from other sources, bookmarks, or from search engines. When seen from this perspective, (which is hard to grasp when your archive contains ten articles) it becomes very important to maintain access to the archives and ensure that links can always be followed. On two occasions I've nearly hosed my database, but my backups saved the day. Never assume your archive of articles and comments will be there tomorrow.

7. You never know who's reading. The vast majority of readers never post a comment or write an email. I should have expected this, since the vast majority of blogs I read never get a comment or email from me. On the other hand, I've met a few very intelligent and friendly people online as a direct result of one or more D-F articles, which is the ultimate reward.

8. Writing begets more writing. Forcing yourself to write regularly about a subject you know about is very therapeutic. More importantly, being forced to back up your arguments in writing on a regular basis makes you examine your own assumptions more carefully. Most important of all, writing regularly brings new ideas into view that you would have missed otherwise.

9. Forget about getting Dugg, try to get StumbledUpon instead. Being a regular reader of Digg, I was well aware of its massive audience and the surge in traffic that follows a site being featured on the Digg home page. The effect usually lasts a couple of days. But the traffic surge produced from a listing in StumbleUpon, continues unabated for weeks, and results in permanently higher overall page views.

10. Robots everywhere. Google Analytics doesn't record activity from robots and web spiders. But my server log reveals a staggering amount of traffic due to non-human visitors. The software interacting with my site is doing everything from indexing it for Google to trying to post annoying ringtone spam comments. Still, the benefit of automated user agents more than outweighs the inconvenience. Make sure your robots.txt file allows any and all user agents.

Image Credit: Seether_Alpha