I’m off to the Society for Developmental Biology’s annual meeting this weekend in Philadelphia. They’ve put together a tremendous lineup this year, and have set up a party in the Mutter Museum. Come say, “hi” if you’re attending, CSHL Press will have a display of recent books and free print copies of CSH Protocols.

Google has officially announced that their Knol product is now open to the public. Over at the Science of the Invisible blog, AJ Cann asks, if it’s worthwhile and really anything “more than extra eyeballs for AdSense.” My response is that of course the whole driving force behind Knol is extra eyeballs for AdSense. That’s what Google does. That’s their MO. To paraphrase the now defunct Fake Steve Jobs, Google’s business model is to drive the price of everything on earth to “free”, everything except one thing that is, small ugly text-based ads, which, conveniently enough, they’ll be the ones selling. So you should never have to ask, is this just a ploy to sell more ads, because with Google, the answer is always going to be “yes”.

That said, there is some merit to the project, and it will be interesting to see if they can get buy-in.
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I’ve given many an “alternate careers in science” talk to groups of students, but I have to say, this one was really my favorite so far. The curriculum director (who happens to be my wife) at Not Just Art, a local science, music and art educational center for children on Long Island, asked me to lend my expertise to the incoming attendees of their Superhero Training Academy (well, Superhero Camp to be more accurate). This should do wonders for establishing the proper geek cred I truly deserve. My lecture on “So you want to be a superhero” can be found below, after the jump.

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Michael Nielsen has written a thoughtful essay over on his blog asking why scientists have been so slow to pick up on new web 2.0 technologies (found via Bora’s blog). It’s good to see that many of his conclusions echo my own (here too), that the big problems are a lack of time and incentive. He offers some potential solutions, and reasons why people should be using these new tools. A few responses, as always attempting to cut through the evangelism, cross-posted over in his comments thread:

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Some very interesting articles have come out in recent weeks, all analyzing the effects of the internet and directly or indirectly discussing the popular “Long Tail” theory, described by its originator as:

“The theory of the Long Tail is that our culture and economy is increasingly shifting away from a focus on a relatively small number of “hits” (mainstream products and markets) at the head of the demand curve and toward a huge number of niches in the tail.”

First up was the widely debated Should You Invest in the Long Tail? by Anita Elberse in the Harvard Business Review. Elberse’s argument is that the data actually shows more and more concentration of markets into hits, that the long tail is extremely flat, and that there seems to be more consumer enjoyment out of the non-long tail material (Chris Anderson responds here, Elberse’s response to him is here).

ReadWriteWeb had a very different article, but one with fairly similar conclusions. In Priming the Pump: New Users, Meet the Old Winners, Marshall Kirpatrick looks at online tech communities, and notes that while online communities are supposed to be “all about the democratization of communication and empowering new voices”, in reality they tend to anoint dieties, with social networks in the tech world, “funneling audiences towards the same major players that dominate other sites…The tech niche of social media is an elitist place.”

How does this relate to science and scientific publishing? Science has published Electronic Publication and the Narrowing of Science and Scholarship by James Evans. Looking at citation data, he notes that the move to online scholarly journals has resulted in a state where “the articles referenced tended to be more recent, fewer journals and articles were cited, and more of those citations were to fewer journals and articles.”
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July’s issue of CSH Protocols includes two highly valuable compendiums of recipes and methods for staining cells, derived from Scion Publishing’s book, Histological and Histochemical Methods (4th Edition). The book is an information-dense treasure trove for cell biologists and microscopists, with over 600 pages of detailed instructions for sample preparation and processing, immunohistochemistry, and the staining of various cell types, tissues, structures and molecules. Nuclear Stains, by John Alan Kiernan covers methods for cationic, anionic, and metal complexing dyes. Anionic Counterstains (also by Kiernan) gives a set of methods for counterstaining with eosin, fast green and metanil yellow. The good folks at Scion have made these protocols freely accessible for both subscribers and non-subscribers, so be sure to take a look.

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I’m staying out of the scuffling on this one. If you follow the science blogosphere at all, you should know by now that everyone is apparently up in arms over the recent Nature article detailing the finances over at PLOS (a follow-up from Nature’s Timo Hannay is here). While many are accusing Nature of deliberately publishing a “hatchet job”, I’ll leave any determinations of intent or malice up to the individual reader.

What’s interesting to me though, is getting to see what’s happening with the economic models of the various open access journals.
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To aid in the study of genetic diseases, the International Haplotype Map Project has developed a haplotype map of the human genome, a tool that displays common patterns of genetic variation. While data from the project are available for unrestricted public use from the project’s website, the new tools needed to browse the map can be difficult to master for the beginner. This month’s issue of Cold Spring Harbor Protocols features a set of articles with clear, step-by-step instructions for the analysis of HapMap data.

Browsing HapMap Data Using the Genome Browser provides details on how to navigate to and explore HapMap data for a gene or region of interest. Written by Albert Vernon Smith, this protocol shows how to analyze a candidate gene to find out whether there are any common single nucleotide polymorphisms (SNPs) in the immediate vicinity, what those SNPs’ alleles are, and the relative frequencies of the alleles in the population. As one of our featured articles for the month, it’s freely available to subscribers and non-subscribers.

The other articles in the set (subscribers only) are Generating HapMap Data Text Reports Using the Genome Browser, Manipulating HapMap Data Using HaploView, Retrieving HapMap Data Using HapMart, and Retrieving HapMap Data via Bulk Download. If your institution does not yet subscribe and you’d like to see these articles, you can sign up here for a free three month trial.