Carbon-based liquid fuels are highly valued for transportation; they are the world's largest form of commercial energy and second largest source of anthropogenic carbon dioxide (CO2) emissions. Strategies to address their CO2 emissions have been shaped by fuel cycle analysis (FCA), a version of lifecycle assessment that examines fuel products and their supply chains. FCA studies have diverse findings and large uncertainties. Disagreements are particularly sharp for biofuels, which are seen as key replacements for petroleum fuels. A critical reading of the evolving literature reveals problems of model structure, including system boundary misspecification, flawed carbon cycle representation, and use of a static framework to analyze dynamic systems. New analytic paradigms are needed for liquid fuels, given their tradability, the realities of the carbon cycle, and the implausibility of capturing carbon from mobile sources. Logical decomposition of options shows that, beyond measures to limit fuel demand, CO2 emissions from liquid fuels must be balanced by increasing the rate of net carbon fixation. Further analysis and discussion are needed of carbon accounting methods, energy research priorities, ways to link CO2 removal options to fuel-related mitigation efforts, and the transportation elements of climate policy.