All depends on what level of meditation you're going for, and how deep you allow yourself to go.
A deep meditative state is very similar to the hypnoidal state, where the conscious mind is in recession (although, without the suggestability of the hypnoidal, as meditation is autosuggestion, rather than external suggestion).
Muscles are relaxed, heart rate is down, and generally, you're awfully close to sleep.
However, it's something that's tunable. When you get used to being able to relax your muscles, clear the mind to a good degree, focus the thoughts on nothing (and that's harder than focussing on something), you can choose what aspects of it you wish..
While sitting at a desk, you can put yourself in a self-sustaining posture (you won't collapse like a rag doll when you relax down). You don't need legs and torso to code, so you relax the muscles there, relax the arms a lot, and clear the mind of all extraneous stuff. If you manage to achieve the 'clear' state of mind, you'll have no trouble refocussing it.
If you're not quite there, still, it helps, as you've just cleared a load of chaff that, even if you didn't realise it, was chattering away at the back of your mind. :)
I guess it's like driving a car. :) you don't go everywhere with the accelerator pedal pressed to the floor.

Malk