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.

Chemistry World is running an article in its December issue titled Surfing Web2O that briefly touches on the subject of chemistry blogs. From analysis to commentary to news gathering, blogging is changing the way large numbers of people relate to each other and the world around them. Why should chemistry be immune to this phenomenon?

One thing that is clear is that scientific blogging, in contrast to traditional scientific publication, is a much more fluid and engaging medium. Roald Hoffman, in his recent Boston ACS talk used the term "ossified" to describe the current state of chemistry publication. Although he went on to talk about how Angewandte Chemie was different, for a split second I though he might start talking about chemistry blogs.

Every new medium has its problems - and chemistry blogging is no exception. First, there's the credibility problem - the perception that the information content of chemistry blogs is somehow innately lower than print journals (a problem that every new medium faces). But beyond this are the much larger problems of understanding how this new medium works, what it can offer you as a participant, and what you might be giving up by participating.

Recent Depth-First articles have touched on some of these subjects:

• Self Referential One of the least obvious side-effects of blogging is that you make it onto Google's radar - big time. How valuable would it be to 'own' the top search terms in your field?

• Advice to Job Seekers From C&E News: Blog Thyself Getting a job: the killer app for scientific blogging?

• Thinking of Starting an Anonymous Science Blog? Five Reasons to Think Again It's a small, small world.

• Ten Things That Surprised Me About Blogging Title says it all.

• Go West Young Man: Does Open Access Really Matter in the Long Run? Why the future of scientific publication may look a lot more like Google, Digg, and Feedburner and a lot less like the ACS.

You may be curious about starting a chemistry blog of your own, but what makes a good one? There are dozens of styles that seem to work, but for me the key qualities come down to a clear purpose (high signal-to-noise ratio), consistency, and attention to detail. Here are some (but by no means all) that I think work especially well:

• Chemical Blogspace This isn't actually a chemistry blog, but rather a chemistry blog aggregator run by Egon Willighagen. Whether you're new to chemistry blogs or not, this is essential reading.

• Molecule of the Day To the point and always on topic.

• In the Pipeline One of the first, and best, in the field. Proof that blogging and working in industry are not incompatible.

• Kinase Pro Analyzing the Kinase patent literature one day at a time.

• Computational Organic Chemistry Companion to a book on the same subject.

• Drugs and Poisons Entertaining, informative, and always on topic.

• The Half Decent Pharmaceutical Chemistry Blog Three words: Saturday Night Synthesis.

• Sigma-Aldrich's ChemBlogs Proof that scientific product marketing can be much more than it currently is. Also see this article.

• A Synthetic Environment Top five lists galore, the history of chemistry, and always something unexpected.

• University of Ottawa NMR Facility Blog Short writeups on NMR.

• Totally Synthetic Chemistry blogs can continue the scientific discussion in real time after a paper has been published. Totally Synthetic offers an excellent model for doing this.

• Carbon-Based Curiosities Chemistry isn't supposed to be that much fun, is it?

New media never succeed by trying to imitate the content or form of established media; they succeed by doing what established media can't. The same is true for chemistry blogging. The established peer-review, publisher-controlled system of scientific communication does many things poorly. Look to blog-like online chemical resources to exploit these weaknesses and thrive.

Image Credit: altemark

If you've ever needed to build a Website hosting mostly static content, you've probably tried out a few Content Management Systems. The problem is not finding them - there must be hundreds. The problem is finding one that successfully walks the fine line between being minimal (so that you can do things your way) and powerful (so that it can grow with your needs).

Radiant CMS is one of those systems. As an added bonus, it's written in Ruby and built on Rails. Radiant succeeds by focusing on the management of pages while providing a powerful extension mechanism.

The Website for my company, Metamolecular, will consist of content produced infrequently (product descriptions and documentation) intermingled with more frequently created blog-like content (updates, tutorials, responses to user questions). Traditionally, the CMS has handled the former, with blogging software handling the latter. But we needed a system that handled both well.

One of the distinguishing characteristics of blogs, as opposed to other kinds of websites, is the unusually large number of similar pages. Handling this kind of content requires pagination - the ability to break an archive up into a series of pages containing a smaller subset of the archive.

Although Radiant doesn't have the ability to paginate its content, it does have a wonderful system for creating extensions. I thought I'd give it a try.

The result is the Paginated Archive extension. It works as a drop-in replacement for Radiant's existing Archive Page. After placing the extension into your PROJECT_HOME/vendor/extensions directory, you'll be able to create and configure Paginated Archives for use with blogs and other kinds of sites generating large numbers of pages. The extension requires Bruce Williams' excellent Paginator gem.

You can get started by downloading the extension here.

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

You know something's gone mainstream when chemistry's flagship magazine, Chemical & Engineering News, recommends it. The current issue contains an article offering five tips for a better job search. And right there at number three is "Connect through blogging."

What specifically should job-seekers be doing with their blogs? The article suggests:

• writing short summaries of your presentations at meetings

• inviting comments to create an interactive environment

• posting fresh content regularly

("Writing summaries of your most recent publications" is not one of the suggestions. Perhaps certain unpleasant copyright issues are best avoided altogether).

I could be dead wrong about this, but the day may well come when not having a professional online presence outside of standard publications will be a competitive disadvantage to chemists. Regardless of whether you're still an undergrad or in your third decade in industry, blogging does something for you as a candidate that is impossible to achieve by other means.

Let me explain.

I've interviewed numerous job candidates, but I find it very difficult to do. No matter how good a company is at pre-screening and structuring the on-site interview, and no matter how skilled the interviewers, the process is fundamentally flawed. Here are some of the things I always looked for but was rarely able to fully address during an interview:

• How passionate is the candidate about their field? Clock-punchers have a tendency to stay in an organization for a long time.

• How does the candidate deal with criticism? The better the working environment, the more likely it is the candidate will be exposed frequently to one form of scientific criticism or another. Dealing with it is not always easy, especially when money and promotions are involved.

• How does the candidate work with potential competitors? Most academic programs in chemistry do very little to prepare chemists for the reality they face in flat, efficient organizations oriented around teams of equivalently-trained peers.

• Can the candidate generate enough new ideas to sustain themselves and anyone who might work with them? A chemist who runs out of good ideas quickly, or who doesn't dig deeply enough when the project is failing will have a very hard time thriving professionally.

• How does the candidate try to persuade others? Persuasion plays a deciding role in getting things done within organizations. Integrity, humility, and tact are incredibly powerful persuasive tools that are only taught by the very best mentors and professors.

• How willing is the candidate to stand against established dogma? Dogma kills innovation. But going against dogma is often very unpleasant, especially for the person doing it. People with the skill and courage to challenge orthodoxy while keeping their cool are worth every penny they earn.

Sadly, no matter what you ask a candidate, you will rarely get good answers to questions like these. For one thing, interviewing is very stressful for candidates, and as surprising as it might sound - it can be equally so for interviewers. For better or worse, what you see during an interview may not be what you would get in a colleague. Another factor is the interview schedule itself and its dampening effect on in-depth discussions.

Blogging, on the other hand, has the unique potential to give insights into all of these questions.

How many blogs do you read by authors you respect but whom you've never met? How many of those blogs offer insight into one or more of the questions listed above? If one of these respected authors were interviewing at your company or university, how would your expectations differ from a candidate you knew less about? How would the quality of the interview differ?

Of course, the effect works in the opposite direction as well. We're just starting to come to grips with the idea that it's literally possible for ordinary people to reach a world-wide audience for virtually zero cost with content that stays around for a long time. The concept is simultaneously liberating and terrifying.

The payoffs can be large for those willing to take the risk, stay creative, focus, and persevere. Which, of course, are exactly the kinds of talents your next employer may be looking for.

Image Credit: blakie