I’m giving a talk as part of a forum on blogging for science publishers later this month and have been digging through the usage numbers for this blog. I was surprised at what I found. From my subjective point of view, I would have assumed that the various posts I’ve done on publishing and Web 2.0 were by far the most read on the site, as those are the ones that have spurred nearly all the discussion here and nearly all the incoming links. The numbers tell a different story. While yes, a few Web 2.0 posts have gotten a lot of attention (they rank 2 and 4 in page hits over the history of this blog), the rest of the top 10 are all science and protocol related (one exception–a post on the 25th anniversary of Molecular Cloning). The most read post on this blog is one about Keller explants (are there really that many Xenopus development labs out there?), number 3 is about BLAST and number 5 is about DNA/RNA Delivery. This was both surprising and gratifying–the main reason we created this blog was to help expose our protocol articles and to help researchers find the material they need to get their experiments done. People are using the blog as a discovery tool. Presumably the entries in this blog turn up in Google searches and are leading readers to CSH Protocols.

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John Sack, director of Stanford’s Highwire Press recently speculated that we may be reaching a tipping point in the hype cycle of Web 2.0, where we’re actually starting to see some practical consideration and thoughtful critical analysis of these technologies, rather than the usual constant stream of evangelism and cheerleading. If so, it’s certainly welcome, and a few recent articles back up his viewpoint:

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Continuing along in the quest to evaluate Web 2.0 tools for biologists, I came across two recent articles, one by web usability guru Jacob Nielsen and one featuring an interview with him. Some valuable points found within:

He offers some cautionary advice on the actual patterns of user involvement on websites that follow the Web 2.0 dictum of having the users create the content:

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Ran into a few very interesting (and very different) articles last week, which I wanted to comment on (more posts to follow).

First up is a blog posting on Sciencebase that quotes chemist (and blogger) Joerg Kurt Wegner, with a proposal that the solution for information overload is to do away with editorial oversight and instead rely on social software. Now, obviously, I’m heavily biased here, and I admit that up front. I’m an editor, it’s what I do for a living, and if I didn’t think I made valuable contributions, I would do something else. That said, there are several problems with Wegner’s proposal.
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This is a presentation I gave last weekend at the Southwest Regional Society for Developmental Biology Meeting. It’s an updated version of an earlier talk posted here. It’s kind of a 180 degrees turn from the previous talk, in that the first one was delivered to publishers, and this one was delivered to scientists. Here I’ve tried to include the thoughtful comments and helpful suggestions that readers made on the first talk, and have also tried to point out currently useful tools and interesting future directions. I don’t come at this subject from the point of view of a programmer, that’s not my background. I’m approaching it as 1) a publisher, who wants to build these tools into our journals and online products to make them more useful, and 2) as a former research scientist, with a thought toward what tools would have made my life easier when I was at the bench. The same caveat applies as last time–I work for a biology publisher, and am a former biologist. My comments and analysis of the culture here refer to that culture specifically (and I’ll try to avoid using the generic word “scientist” where it’s inappropriate). Different cultures have different needs. Certain fields of science collect types of data that more obviously fit in with Web 2.0 approaches. These approaches may not apply directly to the world of wet-bench biology, but they do serve as valuable pointers and directions worth watching. I want to be clear that I’m not writing Web 2.0 off as useless. What I’m interested in doing is separating the wheat from the chaff. Much of what is currently being done under this umbrella is useless and doomed. But there are some gems already available and despite many likely failures, aspects of those failures are worth recognizing and incorporating into future efforts.

If you read the first talk, sorry for the redundancies, and sorry for re-using some of the same jokes. I’ll work on new ones for the next presentation.

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Interesting article out in The Economist this week, which talks about the future of social networking, and Facebook in particular. The central thesis is that aspects of social networking will become ubiquitous as time goes on, but that like web-based e-mail, it’s not something that has much of a business model or a possibility for monetization:

Web-mail has certainly not become a business. Admittedly, Google, Microsoft, Yahoo!, AOL and other providers of web-mail accounts do place advertisements on their web-mail offerings, but this is small beer. They offer e-mail—and volumes of free archival storage unimaginable a decade ago—because the service, including its associated address book, calendar, and other features, is cheap to deliver and keeps consumers engaged with their brands and websites, making users more likely to visit affiliated pages where advertising is more effective.

Social networking appears to be similar in this regard. The big internet and media companies have bid up the implicit valuations of MySpace, Facebook and others. But that does not mean there is a working revenue model. Sergey Brin, Google’s co-founder, recently admitted that Google’s “social networking inventory as a whole” was proving problematic and that the “monetisation work we were doing there didn’t pan out as well as we had hoped.”

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I seem to have been doing a good job of riding the cultural zeitgeist with a recent blog posting, as there have been several writers who have voiced their opinions on their blogs on the subject of reader comments on journal articles. These thoughtful posts are particularly helpful, as I’m giving a talk at a regional Society for Developmental Biology meeting later this month on the subject of online tools and whether any of them are useful. The comments on my earlier talk have been very helpful as well, pointing me toward some great sites like GoPubMed and EpiSpider. I think these mashup sorts of sites, accumulators of information from a variety of sources show great potential. The problem of “I can’t keep up with the literature” is a serious one that Web 2.0 (or whatever you choose to call it) offers relief from. This is certainly a more promising area than yet another “Myspace for scientists” or another Digg clone.

On the subject of readers not leaving comments on papers:
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Kind of an odd editorial in the latest issue of Science. The author, computer scientist Ben Schneiderman coins what he apparently thinks is a new term, “Science 2.0″ (I’m sure he might get a few arguments on that), and defines it as the study of human interactions on the internet. It’s a reasonable enough thesis, that these tools make it easier to study how people collaborate (when using these tools), and it will be an interesting subject. I’m not really sure how relevant it is though, to scientists who aren’t studying human interactions. Researchers need to carefully pick and choose tools that are most likely to be fruitful, to add to their research rather than take away from it by demanding their time and effort. And as Jaron Lanier has pointed out, there are some problems where the group-think inherent to social networks and open collaborations can stifle real progress.

A few interesting articles of note, one on science, the others on the future of publishing:

First, a brutal, but really funny review of a PLOS editorial on advice for graduate students:

“You will be happier if you don’t do things you hate. I must say that this thought never occurred to me before. Also don’t waste 7 years of your life, which admittedly was my first instinct. Good thing I read this editorial.”

Next, Cory Doctorow’s interestingly reasoned take on why stand-alone e-book readers like the Kindle are doomed to failure. He breaks it down in terms of the economics of production, that there simply aren’t enough readers out there to allow the cost of production of these devices to drop (especially when compared with multi-function devices like an iPhone or GameBoy):

“Frankly, book reading just isn’t important enough to qualify for priority treatment in that marketplace. E-book readers to date have been either badly made, expensive, out-of-stock or some combination of all three. No one’s making dedicated e-book readers in such quantity that the price drops to the cost of a paperback — the cost at which the average occasional reader may be tempted to take a flutter on one. Certainly, these things aren’t being made in such quantity that they’re being folded in as freebies with the Sunday paper or given away at the turnstiles at a ballgame to the majority of people who are non-book-readers.”

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Time to add a few links, as some recent articles on online tools for scientists are worth visiting. These include an article on career networking, a warning about the corporate forces behind social networks and an interesting piece by Peter Murray-Rust.

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