The striking features of Jupiter are its colorful bands and its Great Red Spot. The colors seen in Jupiter's atmosphere are not understood. Theorists attribute the colors to sulfur, phosphorus, and carbon-nitrogen compounds.
The atmosphere of Jupiter is difficult to analyze, because it is only observed at high altitude. Unlike Earth, where the effects of Earth's surface on the atmosphere, which are considerable, can be measured to high precision, the deep atmosphere of Jupiter is hidden from the theoretician. Unlike Earth, Jupiter has no surface. The fluid of the atmosphere gradually becomes the H2 fluid of the upper mantle, and deeper in, it may gradually become the metallic hydrogen fluid of the lower mantle. How much the fluid interior affects the convection in the upper atmosphere is unknown. While theories tying the dynamics of Jupiter's upper atmosphere to the dynamics of the mantel exist, successful models based on the concept of a thin atmosphere also exists, and at this time appear to be favored in the community studying Jupiter's atmosphere.
Jupiter has numerous ovals in its atmospheres, with the most prominent being the Great Red Spot. These ovals are vortexes that are associated with pairs of belts. They are anticyclonic, meaning that they are high-pressure systems that rotate counterclockwise in Jupiter's southern hemisphere and clockwise in the northern hemisphere. The smaller ovals are generally white.
The Great Red Spot has appeared red on a number of occasions, but its color varies considerably, and it can appeared gray or white. It drifts in longitude, so it is not anchored to Jupiter's upper mantle, and it rolls between two counterflowing jet streams. The Great Red Spot oscillates in longitude with a period of 90 days.
The temptation is to regard the ovals as similar to hurricanes on Earth, and in fact an early theory was just this. At low altitudes on Earth, a hurricane is cyclonic, meaning that the core has a low pressure. At higher altitudes, however, hurricanes are anticyclonic, because the moist air rising through its center pushes outward at high altitude. From space, therefore, hurricanes appear to be anticyclonic. The signature for this, however, is the movement of air from the center outward. This is not seen in the spots on Jupiter. In fact, the spots on Jupiter have no radial motion of air.
The point about Jupiter's atmosphere, the one feature that makes it radically different from Earth, is that there is no surface to provide friction. This means that if an eddy of circulating air is created, it persists for a very long time because the friction within the atmosphere is very low. There is no mechanism to quickly dissipate the angular momentum that is in an eddy.
Eddies are inevitable in an atmosphere of a rapidly rotating fluid. If a force is exerted perpendicular to the moving fluid of a jet stream, the fluid tries to move perpendicular to that force, very much as a spinning top tries to move perpendicular to an applied torque. So a force exerted perpendicular to the jet steams forces the fluid in that stream to rotate, which creates an eddy.
The eddies themselves can combine over time to produce larger eddies. This is the origin of the white spots; they accumulate eddies at a rate that counters the frictional forces slowing them down. The Great Red Spot is an extreme example of this mechanism; it is no more than a giant eddy that has persisted for centuries.