What are they and where do the come from?

They are bubbles of air. Most gases (including oxygen and nitrogen) are slightly soluble in water at room temperature (that is why fish can live underwater as they extract the dissolved oxygen from the water using their gills). When the water is heated (as for example when you leave a glass of cold tap water in a warm room) the gases become less soluble so they are forced out of the water in the form of tiny bubbles which form on the imperfections in the glass. The fact that oxygen is less soluble in warm water than in cold is a problem for fish in rivers downstream from power stations which often use river water to cool their plant, thus pumping back slightly warmer water into the river. This warm water contains less oxygen and the fish have more difficulty obtaining the oxygen they need.

The bubbles are carbon dioxide, the same as in Coke, Champagne and wee heavy. The gas is soluble in water forming a weak acid. If you leave the water to stand in daylight, the carbon dioxide will from bubbles.