A charged engine may utilize a plurality of independently controllable intake valves for a cylinder of the engine. A method to operate the engine includes monitoring an unmodified timing for the plurality of independently controllable intake valves for the cylinder, monitoring operation of the engine, determining a delayed timing for a first intake valve of the independently controllable intake valves for the cylinder based upon the monitored operation of the engine and the unmodified timing for the plurality of independently controllable intake valves for the cylinder, controlling the first intake valve based upon the determined delayed timing for the first intake valve, and controlling a second intake valve of the independently controllable intake valves for the cylinder based upon the monitored unmodified timing.