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I believe that with the new salt and pepper shakers, the salt shaker is the one with 3 holes, while the pepper goes in the one with 2 holes. Salt is used more than pepper anyway. Pepper should only ever be fresh ground at the table, meaning salt shakers win out.
Many chronic imbalances such as diabetes, gout and obesity can be worsened or even partially caused by excessive intake of common table salt. And be aware, this salt is not just the stuff in your shaker. Most packaged and processed foods contain astronomical amounts of the stuff.