By altering the number, size, and density of particles in the ocean, the activities of different phytoplankton, zooplankton, and microbial species control the formation, degradation, fragmentation, and repackaging of rapidly sinking aggregates of particulate organic carbon (POC) and are responsible for much of the variation in the efficiency of the biological carbon pump. A more systematic understanding of these processes will allow the biological pump to be included in global models as more than an empirically-determined decline in POC concentrations with depth that may not adequately represent past or future conditions. Although progress has been made on this front, key areas needing work are the amount of POC flux associated with appendicularians, the mechanisms by which coccoliths and coccolithophorid POC reach depth, and the impact of polymers such as TEP on the porosity of aggregates. In addition, an understanding of the interaction between biological and physical aspects of the pump, such as aggregate loading with suspended mineral particles, is also important for understanding the transmission of biogenic materials through the meso- and bathypelagic realms. Data suggest that variable biogenic silica to POC production ratios in various ocean regions are responsible for the poor correlation observed between silica and POC in deep sediment traps, and that high concentrations of suspended coccoliths in deep waters may be responsible for the homogeneous calcium carbonate to POC ratios observed in these same traps. Sedimentation of foraminiferal calcite does not appear to be as tightly correlated to POC flux as coccolith sedimentation. Suspended calcium carbonate particles, scavenged by sinking organic aggregates, have been observed to both fragment and increase the density of these aggregates. Analysis of the data suggests that scavenging of minerals by aggregates decreases the porosity of the aggregates and may increase their sinking velocities by hundreds of times.