Can biofuels cause global warming ?

A recent biofuels study published in Science points that the use of natural lands for growing biofuels leads to more CO2 emissions compared to the case where no forest lands are cleared. In an interview about a related topic, another scientist points out that using biofuels over fossil fuels actually increases CO2 emissions because the soil carbon released to the atmosphere. There however are are some ppl who disagree with the study's findings, citing uncertanities in modeling the soil carbon cycle arising out of land use changes (tilling, fertilizer use etc..) as one of the study's main weaknesses. Soil carbon turnover rates in the tropics are be much higher than those in temperate climates. I guess that this is one of the key issues the Science study tried to address; they used a global agricultural model to estimate these emissions. The use of waste biomass (ex: from forests) and producing biofuels without converting additional natural habitats to farmland, will not cause additional CO2 emissions.