Nuclear physics investigates the origin and structure of strongly interacting matter: the atomic nucleus, the proton and the neutron, and the quarks. The interaction between quarks has a remarkable property called asymptotic freedom: it decreases for small distances between the quarks. It is widely believed that quarks do not exist as free particles because a separation is prevented by the growing forces. Unfortunately, the growing coupling strengths make calculations for larger distances virtually impossible. There are two strategies to make progress. Theory has developed lattice simulations of the strong interaction. Experimentally, one studies meson production in nuclear reactions. The Thomas Jefferson National Laboratory has taken a leading role in this field using photonuclear reactions as a probe to produce Baryon resonances and to study their decays in a large energy region ranging from the reaction threshold up to approximately 3 GeV. The extraction of resonance properties from the data at large energies is non-trivial, as one has to take into account the final state interactions between the produced hadrons. Nuclear theory has made progress during the last decade by developing effective theories of meson-baryon reactions that can describe the data.