Charmonium suppression in hot and dense nuclear matter has been argued to be a signature for the production of the quark gluon plasma (QGP). In order to search for this effect in heavy ion collisions one must have a clear understanding of all the fac
tors that can contribute to such a suppression. These may include shadowing of the partons in a nuclear environment, breakup of a correlated $c-bar{c}$ pair as it traverses the nuclear fragment, suppression of feed-down from higher mass states as well as other initial state interactions. In order to disentangle these effects one must measure charmonium production rates in both proton+proton (p+p) and proton+nucleus (p+A) collisions. The p+p collisions serve as a baseline for searching for suppression compared to binary scaling predictions, allow one to quantify the amount of feed-down from higher states as well as serve as a tool to distinguish between different theoretical calculations for charmonium production mechanisms. In order to quantify nuclear effects it is also necessary to study charmonium production in p+A collisions where the temperature and density of the system are low compared to a heavy ion collision. These measurements allow one to determine the influence of nuclear shadowing and breakup in cold nuclear matter which can be extrapolated to heavy ion collisions in order to determine the amount anomalous suppression. Of course, extrapolations that rely on a model based technique depend heavily on the assumption of a production mechanism, a fact that reinforces the importance of the p+p measurements...
The hot nuclear matter created at the Relativistic Heavy Ion Collider (RHIC) has been characterized by near-perfect fluid behavior. We demonstrate that this stands in contradiction to the identification of QCD quasi-particles with the thermodynamic d
egrees of freedom in the early (fluid) stage of heavy ion collisions. The empirical observation of constituent quark ``$n_q$ scaling of elliptic flow is juxtaposed with the lack of such scaling behavior in hydrodynamic fluid calculations followed by Cooper-Frye freeze-out to hadrons. A ``quasi-particle transport time stage after viscous effects break down the hydrodynamic fluid stage, but prior to hadronization, is proposed to reconcile these apparent contradictions. However, without a detailed understanding of the transitions between these stages, the ``$n_q$ scaling is not a necessary consequence of this prescription. Also, if the duration of this stage is too short, it may not support well defined quasi-particles. By comparing and contrasting the coalescence of quarks into hadrons with the similar process of producing light nuclei from nucleons, it is shown that the observation of ``$n_{q}$ scaling in the final state does not necessarily imply that the constituent degrees of freedom were the relevant ones in the initial state.
