  Motivated by recent developments in the AdS/CFT correspondence, we provide
several alternative bulk descriptions of an arbitrary Wilson loop operator in
Chern-Simons theory. Wilson loop operators in Chern-Simons theory can be given
a description in terms of a configuration of branes or alternatively
anti-branes in the resolved conifold geometry. The representation of the Wilson
loop is encoded in the holonomy of the gauge field living on the dual brane
configuration. By letting the branes undergo a new type of geometric
transition, we argue that each Wilson loop operator can also be described by a
bubbling Calabi-Yau geometry, whose topology encodes the representation of the
Wilson loop. These Calabi-Yau manifolds provide a novel representation of knot
invariants. For the unknot we confirm these identifications to all orders in
the genus expansion.
