I’ve written about Zotero before, it’s an intriguing tool, essentially a Firefox plug-in for managing your reference list and other pieces of information. It’s a bit of a hybrid between online management tools like Connotea and things like Papers which you store on your own computer.

The bad news is that Thomson Reuters, the manufacturers of EndNote, are suing George Mason University and the Commonwealth of Virginia because a new version of Zotero lets you take your EndNote reference lists and convert them for use in Zotero. Yes, this is the same Thomson of Thomson ISI, secret gatekeepers of journal impact factors. They really seem to be going out of their way to lose what little goodwill they have left with the scientific community. It will be interesting to see if this reverse engineering for interoperability holds up in court as something that should be prevented.
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Some interesting recent articles on Web 2.0 and Publishing:

EmTech inanity
Ever since Dan Lyons abandoned his Fake Steve Jobs persona, his blog has gone way downhill (and his Newsweek articles have been generally lame as well). But when he fires on all cylinders, he can still put out some of the funniest, most scathing commentary you’ll find on the tech industry. Here he reviews a conference panel of some of the biggest names in Web 2.0 and really nails the failings of so many of these tools, particularly those launched for scientists: they’re solutions in search of problems:

“If I were funding these guys I might go home scratching my head about what those kids are doing with all of my millions. Maybe there is a point to what they’re doing, but honestly, what great problem are these companies trying to solve? Sitting there watching this spectacle — watching these guys unable to simply explain what they do and and how they are going to make a business out of it – it was staggering to think that someone has entrusted these people with very large sums of money.”

Lyons further hammers home his message by noting that the participants all spoke about “how they had been trying to find a good restaurant in Boston and how their cool social networking tools and collaborative filters had enabled them to do such a great job of this restaurant hunting task.” The restaurant they found? The Union Oyster House, a dreadful tourist trap that anyone who has lived in Boston knows to avoid. Also, the quote of the week can be found in the article’s comment section:

“…the unspoken agreement of Web 2.0 seems to be that there is nothing more terrible than having to spend even a second alone with one’s own thoughts.”

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Recently, the NY Times had an article discussing the concept of “ambient awareness”, or as the article puts it, “incessant online contact”. Now, first off, I have to admit that I’m one of the over-30-year-olds the article mentions, who finds the concept of subjecting others to (and being subjected to) a stream of trivial details about one’s day completely unappealing. The proponents of Twitter and FriendFeed and the like feel that they’re getting a more intimate understanding of people, “something raw about my friends,” as one user puts it. I’m more in line with the critics quoted in the article that the end result is more “parasocial” than social, and that it ends up an extension of reading gossip magazines and following celebrities from afar.

So how do these new practices apply to the world of science research?
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John Mundy’s laboratory at the University of Copenhagen has written up protocols for Coimmunoprecipitation (co-IP) of Nuclear Proteins and Chromatin Immunoprecipitation (ChIP) from Arabidopsis in the September issue of CSH Protocols. co-IP is useful for identifying and isolating protein-protein interactions and protein complexes. ChIP allows the analysis of protein-DNA interactions, and is a technique currently seeing widespread use as the field of transcriptional regulation continues to make great advances. One advantage to this set of techniques is that the nuclear lysis buffers standard in most protocols for plant nuclear protein extraction are incompatible with co-IP. Here, nuclear protein extraction is accomplished via sonication in co-IP buffer and treatment with Benzonase, which results in material that can be used with co-IP.

As always, catching up with some interesting articles regarding publishing, science and Web 2.0:

Beyond the Flickering Screen: Re-situating e-books
An excellent article, and one of the best, most realistic takes I’ve seen on the future of e-books. The author argues that while cost plays some factor in the failure of e-books to catch on (a Kindle purchaser needs to buy 61 books before they break even on the purchase of their device), the real problem is a cultural one:

“The idea of electronic books, or e-books, remains the domain of geeky early adopters. The reasons for this are manifold, but, arguably, a broader uptake of e-books has not occurred because cultural change is much more difficult than technological change and book readers have yet to be persuaded to change their cultural habits.”

He suggests that one solution for this is to make e-books ubiquitously available, rather than limiting them to a separate e-book-reader-only ghetto. To reach a mass audience, e-books need to be a common part of the sort of things one does online or with the electronic devices one already owns:

“The availability of e-books on mobile platforms may not result in more people embracing longer-form literature. But it will increase the number of people actually reading, and, just as casual gaming has attracted a female demographic, the instant availability of appropriate reading material might sway some of those men who appear to be reluctant readers.
Rather than focus on printed books, and book-like reading devices, the industry should re-position e-books as an easily accessible content choice in a digitally converged media environment. This is more a cultural shift than a technological one—for publishers and readers alike. Situating e-books in such a way may alienate a segment of the bookloving community, but such readers are unlikely to respond to anything other than print on paper. Indeed, it may encourage a whole new demographic—unafraid of the flickering screen—to engage with the manifold attractions of “books.””

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The September issue of CSH Protocols is now available online, and this month brings a set of nine protocols from Renee Reijo Pera’s laboratory at Stanford describing methods for the generation, maintenance and analysis of human embryonic stem cells (hESC). With the upcoming presidential elections, and both candidates favoring expanding federal funding for stem cell research (and one vice presidential candidate agrees, the other, not so much), the near future should see increased usage of these valuable research techniques. Two of these hESC protocols are featured in this month’s issue (our featured protocols each month are available to subscribers and non-subscribers alike).

Noninvasive Human Nuclear Transfer with Embryonic Stem Cells describes the transfer of a nucleus from a somatic cell to an enucleated oocyte for reprogramming to an embryonic cell state. Older methods commonly use Hoechst and UV light, which can lead to DNA damage. Here, a polarized microscopic imaging system is used to visualize the meiotic spindle without DNA staining and UV illumination.

Culturing Human Embryonic Stem Cells in Feeder-Free Conditions describes the culture of hESCs in feeder-free conditions on Matrigel with MEF-conditioned medium. This protocol can be used for applications such as genetic modification of hESCs without feeder cell contamination.