Leg 199 was designed to study the equatorial Pacific in the early Cenozoic. In particular, the leg was drilled to understand how the equatorial Pacific responded to warm early Cenozoic global climate and how biogeochemical and physical processes of the equatorial Pacific helped to contribute to global warmth. A secondary goal was to understand how the equatorial Pacific changed as ice sheets grew on Antarctica.

Earth experienced a generally warm climate prior to 33.6 Ma, termed the "Greenhouse world" (e.g., Miller et al., 1987), which lasted until just after the end of the Eocene (the Eocene/Oligocene boundary is currently dated at 33.7 Ma). An oxygen isotope event known as Oi-1 beginning at ~34 Ma marked the appearance of extensive permanent ice sheets on Antarctica and the beginning of the "Icehouse world" (Miller et al., 1987; Zachos et al., 2001; Coxall et al., 2005). The brief Oi-1 glacial interval had a maximum advance now dated at 33.6 Ma (Coxall et al., 2005; Pälike et al., unpubl. data). Roughly half of the Cenozoic, then, was significantly warmer than modern conditions. Additional information about the Cenozoic evolution of the Pacific can be found in Lyle et al. (submitted [N2]). Carbon cycle changes over the Cenozoic are large in comparison with those of the Holocene or Pleistocene. The beginning of the Cenozoic was marked by atmospheric CO2 concentrations perhaps 4 to 5 times higher than modern atmospheric CO2, contributing to early Cenozoic Greenhouse conditions (Pearson and Palmer, 2000; Demicco et al., 2003; Royer et al., 2004). Somewhere near the end of the Eocene or beginning of the Oligocene, atmospheric CO2 content began to drop to near-modern levels (Pagani et al., 2005) and may have been a driver for the Greenhouse–Icehouse transition at the Eocene/Oligocene boundary. It is not possible with current data to show that the E/O cooling was caused by greenhouse gases, but all proxies agree that atmospheric CO2 levels were high in the Eocene but dropped to near modern values by the end of the early Miocene (Pagani et al., 1999; Pearson and Palmer, 2000; Royer, 2002).

Feedback mechanisms from the carbon cycle are probably needed to maintain warmer than modern conditions in the Eocene. A modified carbon cycle is also needed to maintain the high atmospheric burden of greenhouse gases prior to 34 Ma. Because atmospheric CO2 and methane concentrations probably have varied by large factors over the Cenozoic, the Paleogene provides a useful testing ground to study greenhouse gases and climate at tectonic, orbital and climate "transient" timescales. Climate transients like the PETM (Kennett and Stott, 1991; Dickens et al., 1995; Norris and Röhl, 1999; Thomas, 2003; Thomas et al., 2003; Zachos et al., 2003, 2005) provide an important means to study how the Earth responds to large short-lived changes in greenhouse gas concentrations forced by the release of fossil carbon. Carbon cycle and climate responses to the periodic changes in insolation caused by orbital variations (Laskar et al., 2004; Pälike et al., 2004) provide a way to monitor climate sensitivity under altered base conditions.