Back in 1970 Richard Baker fell in love with John McConnell. They applied for a marriage license in Minneapolis. Gerald Nelson, the county clerk, denied their request. Baker sued for a license in a case known as Baker v. Nelson. He lost every step of the way through the Minnesota Supremes. In 1972 the federal Supremes responded to the appeal by saying, "The appeal is dismissed for want of a substantial federal question."
In layman's terms that means the Supremes said they didn't have jurisdiction because the issue didn't involve federal law or the Constitution (remember this is 1972). That dismissal has been dogging marriage equality cases ever since, with cases arguing why Baker no longer applies.
Baker and McConnell eventually found a clerk to issue a license and a pastor to perform the ceremony. The two haven't been involved in the recent marriage equality cases because they consider themselves having been married since about 1972.
That brings us to the marriage equality case from Puerto Rico. Ari Ezra Waldman of Towleroad explains the importance. First, since the Supremes haven't ruled on a marriage equality case Baker is still in effect as their last word. Second, Circuit and especially District courts are reluctant to challenge a ruling from above, which is why we didn't get a flurry of rulings until after the DOMA case last year. So the judge in Puerto Rico who denied hearing a marriage equality case could be said to be following the instructions from the Supremes.
Waldman goes on to document the legal progress we've made since 1972 and how that allows many District and Circuit courts to dismiss Baker and its implications.
That Puerto Rico case is headed to the 1st Circuit. All the states in the 1st Circuit already have marriage equality so that Circuit hasn't ruled on the matter. Also, the 1st Circuit upheld Baker just two years ago. Perhaps the 1st Circuit will set up the conflict that will prompt the Supremes to take a marriage equality case – if the 5th or 6th Circuits don't get there first.