The Guardian posted a leaked letter (worth reading and mulling over in its entirey) from Seed Media Group CEO and Seed magazine editor Adam Bly, which admitted that Pepsi’s blog was a strategic financial deal [links added]:

SB, like nearly all free content sites, is sustainable because of advertising. But advertising is itself highly unpredictable, as the last year has shown the industry. And securing advertising around topics like physics and evolution is even more challenging as the dearth of ad pages in science magazines indicates. We started experimenting with sponsored blogs a couple of years ago and decided to market long-term sponsorship contracts instead of sporadic advertising contracts. This is not a new idea: respected magazines have been doing the same thing for years (think Atlantic Ideas Festival going on now or The New Yorker Festival, where representatives of sponsoring companies sit on stage alongside writers and thinkers, or advertorials where companies pay to create content — clearly marked as such — instead of just running an ad). But we accept that we haven’t got it 100% yet. Should we host these blogs under a modified SB logo? Allow our readers to exclude them from RSS feeds? Establish a blogger council that signs off on the scientists who are blogging? Make the sponsor’s logo clearer on the banner? As always, I would very much welcome your feedback and suggestions so we can build a stronger SB for the future. It’s in our collective interest to ensure the long-term sustainability of a mission that we all believe is important.

That may be so, but there is a limit to what even full transparency can accomplish. While conferences like the ones Bly cites are indeed rainmakers for the media industry, such events are quite a bit different than renting out space in a science/journalism community that values impartiality and abhors corporate influence.

[Update, 9:30 a.m.: In the comments section of Paul Raeburn’s post at the Knight Science Journalism Tracker, there is an interesting discussion about previous “corporate blogs,” as Bly put it in his letter sponsored by GE and Shell. Stacey and another current Scienceblogs.com member, Josh Rosenau, think the companies had less control over those blogs, but that seems uncertain. Additionally, NPR’s Ira Flatow offered to host defecting bloggers at his Science Friday Web site.]

Science journalist and author Carl Zimmer, whose Discover blog, The Loom, once resided at ScienceBlogs.com, took Bly to task for ruining years of hard work:

What I find particularly galling about this whole affair is that bloggers who don’t want to associate themselves with this kind of nonsense have to go through the hassle of leaving Scienceblogs and setting up their blog elsewhere. The technical steps involved may be wonderfully easy now (export files, open account on Wordpress, import), but the social steps remain tedious. Take it from me, someone who has moved his blog three times over the past six years: your readers lose your trail, and it takes a long time for Google to start helping them. These folks did nothing to deserve this irritation.

Zimmer is also keeping a running list of Sciencblogs.com defectors. If begins to grow, we’ll see how Bly responds. One hopes that he and his colleagues at Seed Media Group were sitting around a table late Wednesday night re-thinking their approach.
Fundraising is a legitimate problem in the industry today, but a smart play would be to put the Pepsi blog on hold and reach out to bloggers for ideas. It would be a tragic shame to break up an honest, insightful, and widely respected community of writers for something as foolish as Food Frontiers.

[Update, 10:30 a.m.: Bly just announced that Scienceblogs.com has taken down the Food Frontiers blog, writing, “We apologize for what some of you viewed as a violation of your immense trust in ScienceBlogs. Although we (and many of you) believe strongly in the need to engage industry in pursuit of science-driven social change, this was clearly not the right way.”

Curtis Brainard is the editor of The Observatory, CJR's online critique of science and environment reporting. Follow him on Twitter @cbrainard.