The behavior of red wine in cooking is complex. When cooked with foods that contain protein, such as fish or meat, the tannins and pigments in the wine combine with the proteins that are released during cooking. This clarifies out much of the color and acidity, and any astringency due to the tannins will disappear. Specks of pigment are often visible in the sauce and, if need be, can be strained out.
Red wine reduced alone or with flavor components that contain no protein, such as onions, garlic, or a bouquet garni, will be entirely different from wine that is cooked with meat, fish, or stock. Protein “clarifies” the wine’s acids and tannins; red wine reduced in the absence of protein will retain harsh tannins and acids Hence, when making a red wine sauce containing meat or fish stock, simmer them together, not separately.