The mature information worker is someone who can manage his queues effectively, prioritizing and re-prioritizing as new items crop up, doing the fast-context-switching necessary to respond to an email while waiting for a file to download or a backup to complete. It's a little like spinning plates, and when you get the rhythm of it, it can be glorious. There's a zone you slip into, a zone where everything gets done, one thing after another clicking into place.
But once you add an interruptive medium like IM, unscheduled calls, or pop-up notifiers of mail, flow turns into chop. The buzz, blip, and snap of a thousand alerts turn plate-spinning into hell, as random firecrackers detonate over and over again, on every side of you, always there in your peripheral vision, blowing your capacity to manage your own queue as they rudely insert themselves into your attention.
This point truly resonates with my experience and my aversion to instant messaging. It kills my flow, and it can take a while to get this flow back.
A good way to mitigate negative the effects of interruptible communcation on the desktop in the instance that IM is a requirement is to use multiple computers. When you want to do something important, use the computer without an IM client, and make sure any auditory alerts are disabled.