TECHNOLOGY FOCUS - INORGANIC CHEMISTRY - Preferred Components: The porous substrate comprises activated carbon, carbon foam, alumina, gamma alumina, silica-alumina, metal foam, silica, zeolites, titania, zirconia, magnesia, chromia and/or monoliths. The porous substrate is granular and comprises activated carbon, alumina, silica-alumina, silica, zeolites, titania, zirconia, magnesia and/or chromia. The porous substrate is granular activated carbon. The metal comprises palladium; nickel; or chromium, molybdenum, tungsten, iron, ruthenium, osmium, cobalt, rhodium, iridium, platinum, zinc, copper, silver and/or gold. The metal is oxide free. The catalyst is catalytically active for hydrogenation and preferential deoxygenation by decarbonylation and decarboxylation over hydrodeoxygenation. The catalyst is catalytically active for hydrogenation and preferential deoxygenation of triglycerides by decarbonylation and decarboxylation over hydrodeoxygenation. The catalyst is catalytically active for hydrogenation and preferential deoxygenation of alcohols, ethers, aldehydes, ketones, carboxylic acids, esters and/or phenolics by decarbonylation and decarboxylation over hydrodeoxygenation. The substrate has pores 0.2-10 nm wide and the metal present in that.    TECHNOLOGY FOCUS - INSTRUMENTATION AND TESTING - Preferred System: The system further comprises a three-phase separator configured to receive effluent from the deoxygenation stage and to separate water, liquid hydrocarbons, and gases from the effluent into separate streams; a second separator to receive the gases to separate hydrogen from carbon monoxide, carbon dioxide, and light gases; and a reformer and shift reactor to produce hydrogen from the carbon monoxide and the light gases. The system further comprises a hydrocracking and isomerization stage containing at least one hydrocracking and isomerization reactor and a hydrocracking and isomerization catalyst, where the hydrocracking and isomerization stage is configured to receive deoxygenated liquid hydrocarbons and hydrogen. In the system, the deoxygenation stage comprises at least two deoxygenation reactor chambers connected in series and a separator to remove carbon monoxide, carbon dioxide, water, and light gases between the deoxygenation reaction chambers. In the system, the deoxygenation reactor chamber and the catalyst are configured as a packed bed reactor to operate in continuous multiphase flow mode with hydrogen as a reactant.