I think it's nowhere near as bad as the article sounds. The red square from Google+ is small and hidden in the place I usually don't even look, so I find myself not realizing for days that got a notification from Google+. On Facebook, notifications are one of the most useful features of the whole service - they tell me about the more important[1] events that I could otherwise miss (Facebook walls are heavily filtered; otherwise you'd be flooded by updates). And they don't even appear on your e-mail, unless I ask for it (Facebook has now disabled almost all e-mail notifications by default).

So I'm sorry, but I'm not convinced by this article. On the contrary, I find notifications to be one of the best UI solutions out there. They are completely noninvasive[2] and make sure you don't miss anything, so you don't have to constantly check what is going on. It boils down to what alexchamberlain said in the thread - event-based architecture beats polling in almost all cases.

[1] - if we can call anything on Facebook "important". But things like comments to my updates, or activities of my closest friends are things I don't want to miss.

[2] - Twitter, G+ and Facebook notifications are generally numbers on the webpage title / notification bar. They do not play sounds, they do not pop windows up. If one gets distracted by that, I recommend not keeping FB/Twitter/G+ tabs open in the browser during work.