J.L. Vernon echoes many of the points I made in Are Science Blogging Networks Dead? but also focuses on a distinct aspect, writing Just like the NBA, “Science” is a brand.  It's a message that may be lost on some, or they would self-police a little better and certainly ask their commenters for a little more maturity - but it may be that while science is a brand (Science 2.0, Discover, Nature, etc. certainly always want to make sure writers get benefit beyond traffic from being in respective publications) at Scienceblogs, bloggers are themselves the brand.

This independence from the brand was affirmed numerous times during the Pepsigate thing but also again today on Greg Laden's blog, which didn't think much of my "Are Science Blogging Networks Dead?" article, by a person who wrote "I never thought of scienceblogs as a network with any added value from the community end of it. To me it is just a somewhat more organized RSS feed."

They all came from independent sites and had to be popular enough to add to the advertising revenue rather than just dilute impressions so it's understandable if they do feel that way, though neither I nor a commenter from there can make that determination.  Without question, a number of them certainly did feel like they had a personal brand but a stake in the Scienceblogs one as well.   The bulk of those who left did so because they felt like they had built the brand and it was being corrupted to make a buck.

But if so, why didn't they protect it better before then?   Vernon discusses the Heffernan NY Times piece which was chock full of Tweet-worthy insults (as long as they aren't directed at me, that is) and missed the mark in some spots, but it was dead on in stating that there was a lot of invective over there and it was easy to miss the good stuff.  Here is what he thinks as to why no one internally said anything until it boiled over: 

When constructing her image of science bloggers in a recent NYT article,
Virginia Heffernan went one step too far and made the embarrassingly
ignorant mistake of lumping all science bloggers together with some of
the nastiest personalities on the net.  It is undeniable, though, that
some of the most malevolent bloggers are also the most prominent. 
Sadly, these folks are welcomed, even adored, by their more
mild-mannered network partners.   And, much like trashy personalities
have come to dominate the entertainment industry, this particular brand
of blogging is among the most “popular.” Since “popularity” equates to
viewership, the network hosts tend to allow them to rule the roost.  I
wonder how much of the acceptance of our more unpleasant virtual
neighbors also stems from a fear of retribution for trying to rein them
in.  The costs of confrontation with these “blogfathers” can be
devastating.

It's true that if you want to be liked by big bloggers you admire you have to keep criticism in check but the researchers and book authors who write in most places, their own or sites like this, don't even really know who popular bloggers are so plenty of sites have done well without catering to people who foment controversy.

At a time when policy decisions are increasingly dependent on

scientific solutions, it is important that the “Science” brand be

strong.

Ask the 99.99% of climate researchers doing terrific work what it is like when the brand is tarnished by a few bad eggs and that is exploited by detractors.  It is no different for any other public policy issue.    Scientists can't be expected to be viewed as neutral experts at some times while they are acting like militant kooks in others - and as blogging continues to gain legitimacy, perhaps even as citations - it will become more important than ever not to just circle the wagons around people who have the same URL, but to stand up for quality and dialogue.