TECHNOLOGY FOCUS - ORGANIC CHEMISTRY - Preferred Method: In the method (m1), the step of modifying the first loop involves increasing the amount of exhaust gas recirculated if the amount of biomass-derived fuel increases. In the method (m1), the step of modifying the second loop involves increasing the amount of fuel provided if the amount of biomass-derived fuel increases, where the increasing includes increasing the duration of the main fuel pulse, maintaining the end of the main fuel pulse at the same position relative to the engine cycle, and maintaining the start of the main fuel pulse at about the same position relative to the engine cycle; and moving forward within the engine cycle the pilot pulse of fuel if the amount of biomass-derived fuel increases. In the method (m1), the step of providing involves disposing an oxygen sensor within the exhaust of the engine; and the step of estimating involves using a signal received from the sensor. In the method (m2), the controller uses the estimated energy content to modify a fueling schedule; and the step of providing involves use of a wideband oxygen sensor for measuring oxygen content of the engine exhaust gas, and the estimating step involves use of a measurement from the sensor. In the method (m2), the operating step involves increasing the duration of a pulse of fuel if the energy content of the fuel decreases, providing increases fuel earlier in the engine cycle if the energy content of the fuel decreases, and moving forward within the engine cycle the pilot pulse of fuel if the energy content of the fuel decreases. In the method (m3), the modifying step involves calculating a desired quantity of exhaust gas to recirculate into the engine. The loop limits the oxides of nitrogen in the exhaust gas from the engine. In the method (m3), the step of providing involves use of a valve actuatable to control the flow of recirculated exhaust gas, and the modifying step is carried out by actuating the valve. In the method (m3), the calculating step is carried out by using the estimated fuel flow rate, estimated oxygen content, and estimated air flow rate. The method (m3) further involves estimating the rate of flow of recirculated exhaust gas into the engine with the controller, and the calculating step is carried out by using the estimating the flow of exhaust gas recirculation (EGR), where the estimating the rate of flow of recirculated exhaust gas involves estimating the oxygen content of the recirculated exhaust gas. In the method (m3), the estimating the oxygen content of the fuel involves measuring the oxygen content of the exhaust gas from the engine, where the measuring oxygen content is with a wideband oxygen sensor; and the estimating the rate of fuel flow involves measuring the rate of fuel flow, and estimating the rate of ambient air flow involves measuring a quantity corresponding to the rate of airflow. In the method (m3), the engine operates with compression ignition of the fuel, or with spark ignition of the fuel; and the rate of fuel flow is a desired rate of fuel flow. The compensating step involves beginning the injecting of a pulse of fuel earlier in the engine operating cycle; ending the injecting of a pulse of fuel later in the engine operating cycle; and increasing the pressure of fuel provided to the injector. In the method (m5), the modifying step is carried out by changing the timing of a discrete pulse of fuel provided for combustion in the engine, where the timing is of the start or the end of the pulse of fuel; or by changing the pressure of fuel provided to the injector, where the timing of the pulse is substantially unchanged; or by injecting a pilot pulse of fuel earlier in the engine cycle. The method (m5) further involves injecting pulses of fuel during the engine cycle, where the modifying is by increasing the duration of at least one of the pulses if a lower energy content is estimated. In the method (m6), the step of providing involves use of a valve actuatable by the controller to control the flow of recirculated exhaust gas, and the modifying step is carried out by actuating the valve. In the method (m6), the operating is with an oxygenated fuel and the calculating includes using the estimated rate of fuel flow into the engine. In the method (m6), the calculating step includes estimating the oxygen content of the recirculated exhaust gas, and the step of estimating the oxygen content of the fuel involves measuring the oxygen content of the exhaust gas from the engine, where the measuring oxygen content is with a wideband oxygen sensor. In the method (m6), the engine operates with compression ignition of the fuel; and the fuel includes biodiesel. Preferred Components: In the method (m3), the fuel includes biodiesel or is a blend of a petroleum-based fuel and a biomass-derived fuel; and the quantity is manifold pressure or engine speed. EXAMPLE - No suitable example given.