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I am too. I wrote up a brief note about how that might work here: http://tomvladeck.com/2013/10/04/twitter-conversation/

I always suspected that was the reason behind disqus.

we once tried to play in a corner of that space as well (focused more on expertise/ context), but it is clearly a chicken & egg situation.

How would that work? Wouldn't it essentially be replying to a master tweet from the website (assuming the website auto-tweeted new submissions, something that many sites do now)?

It could just be a comment thread 1 level deep, a la the current Twitter Conversations implementation. The website can prompt the user to syndicate the Tweet to their stream. (This is also how Facebook Comments work.)

would you really use a commenting system on your site in which people can only reply with 140 characters?

For comments, it would cut off the display on Twitter at 140 characters, with a link to view the full comment on the external site. This would also encourage site owners to adopt the system, as Twitter would push tons of traffic.

I wouldn't necessarily want every comment I write to become a tweet. Like this one, for example