The presence of direct higher-twist processes, where a proton is produced directly in the hard subprocess, can explain the "baryon anomaly" -the large proton-to-pion ratio seen at RHIC in high centrality heavy ion collisions. Direct hadronic processes can also account for the deviation from leading-twist pQCD scaling at fixedRescattering interactions from gluon-exchange, normally neglected in the parton model, have a profound effect in QCD hardscattering reactions, leading to leading-twist single-spin asymmetries, diffractive deep inelastic scattering, diffractive hard hadronic reactions, the breakdown of the Lam-Tung relation in DrellYan reactions, nuclear shadowing -all leading-twist dynamics not incorporated in the light-front wavefunctions of the target computed in isolation. Antishadowing is shown to be quark flavor specific and thus different in charged and neutral deep inelastic lepton-nucleus scattering. Other aspects of quantum effects in heavy ion collisions include hidden color in nuclear wavefunctions, the use of diffraction to materialize the Fock states of a hadronic projectile and test QCD color transparency, and the important consequences of color-octet intrinsic heavy quark distributions in the proton for particle and Higgs production at high x F . The "ridge" -the same-side long-range rapidity correlation observed at RHIC in high centrality heavy ion collisions is suggested as due to the imprint of semihard DGLAP gluon radiation from initial-state partons which have transverse momenta biased toward the trigger. I also discuss how the AdS/CFT correspondence between Anti-de Sitter space and conformal gauge theories allows one to compute the analytic form of frame-independent light-front wavefunctions of mesons and baryons and to compute quark and gluon hadronization at the amplitude level. Finally, the BLM method for determining the renormalization scale in pQCD calculations is reviewed.