So this is what the Democrats have to do: they have to figure out how to defend a value system based on tolerance, compassion, science, and empiricism -- and express it in stark, dramatic, symbolic terms. The Democrats need to work on promoting this vision across the whole range of institutions that they still largely control.
In the short run, i.e. over the next four years, this means that the Democrats need to get very strategic about picking which opposition battles they want to fight. They need to be careful, because they need to realize that they are going to lose every battle they fight, and in order not to get painted as mere obstructionists or whiners, they need to focus on a key symbolic battles, while more or less ceding the rest of the field. They should only fight battles where the issues can be expressed in clear, consistent, symbolic terms, and that unambiguously signify that the Democrats stand for a scientific, tolerant, open society in contrast to the GOP's belief in anti-scientific intolerance.