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If your economics correspondent reckons there is more money to be made by not being in your newspaper then you have to start thinking about your business model.
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It could be that the business model is less suited to correspondents who have their own brand. Bringing the this particular blog into the NYT fold probably helped both a little but I am betting that the ongoing costs to the Freakonomics brand were getting to be a bit much (e.g. myself and probably thousands of others who dropped the freakonomics blog when the stopped providing full RSS feeds.)
Just like syndicated cartoonists - it is interesting though that a major print newspaper isn't as good as a blog once you have your own book out.
You assume that economists know anything about making money. They usually don't (although they love to pretend they do).
The point Dubner made in the blog post is, I think, a valid reason to leave. It used to be that Freakonomics was a book with a follow-up blog trying to build/retain an audience for book #2. In that context, getting NYT to provide the platform makes a lot of sense. But when you're tossing in a whole lot of multimedia stuff and films and podcasts, it starts to make sense to run your own show.

Sort of like when you're starting up, it might make sense to run stuff on VPSes and shared servers and cloud or whatever, but as you scale, the incentives to own your own boxes triumph.

Freakonomics is not in the newspaper. The newspaper refers to the print edition. Freakonomics is however in a profitable and highly trafficked web site.

The NYT web site business model works pretty well, but not enough to support the entire newsroom operations. However, the print side of the company still creates revenue to cover all that. The question is what business model will support that as print declines.

To your larger point I also disagree. They discuss their other ventures that they own (book, radio etc) which isn't owned or related to the Times. Therefore I'm guessing it's difficult for them to cross promote efficiently and drive people to different places. Moving to freakonomics.com makes perfect sense.

The podcast mentioned in the article is excellent. I think the HN crowd would really enjoy listening.
Now if 538 can see the light and go back to being independent...
It's about time. I love this blog but stopped reading it when they went to the NYT and stopped providing a full RSS feed. That was years ago!
I did the same. They also started pumping out too much content and added too many additional authors. I loved reading their blog posts, but it became work to keep up with everything.
YES. This is one of numerous sites that I love that I flat-out don't read because of a lack of full-text RSS.
There have been unofficial full-text feeds for just as long...
Didn't anybody tell these guys that economics is boring? You can't sell many books about that. Or a DVD (available today).

Inspiring to me.

They're really writing sociology for the most part.
Isn't that the point of their book (and also books by guys like Steven Landsburg), what we call economics is really just sociology applied to buying and selling things.
You're right, there's a lot (if not the vast majority) of applied sociology that masquerades as philosophy and/or economics.
I was an avid reader of Nate Silver's from the moment in 2008 that I noticed he was figuring things out about the Obama v. Clinton race ahead of everyone else. When his blog went to the NYT I thought, "good for him". But just a day or two ago I finally admitted to myself that somehow, being at the NYT has made it lame. I've stopped reading it, even stopped checking it. I doubt that Nate has gotten dumber. It must be something about the NYT.
I have had pretty much the same experience, though I can't say for sure how much of my behavior is due to the 2008 election season being long over.
Oh man, there goes all that PageRank from when they mentioned my site!