You should be doing regular exercise anyway, but I think the greatest damage in lying all day is done to the small support muscles. These muscles (like your abs

You should be doing regular exercise anyway, but I think the greatest damage in lying all day is done to the small support muscles. These muscles (like your abs) are design for a constant level of moderate engagement, like walking, and sitting does engage these muscles to a moderate degree, particularly if you are sitting 'properly'. As a comparison, I'm thinking of the difference between slouching in a chair vs. sitting up. If we mapped these on a scale of what is best for you, I'd say that lying down is probably better than slouching, but sitting up is going to be best. These are just my thoughts, I'm not a doctor or physiotherapist.