Though Tolkien might have been familiar with physics, I really doubt he had them in the back of his head when he wrote the Music of the Ainur. There are probably parallels to other myths of creation, I don't know. Regardless, I just happen to think that the creation of the world by music is a breath-takingly romantic idea. It doesn't deserve to be spoiled by cold science.
Concerning the meaning of the Second Theme, I came to believe that it signifies the Marring of Arda.
The First Theme starts as the Creation of Arda in perfection. Then Melkor tries to bring in his own stuff and it ends in chaos. If there was no second theme and the Music continued with the third now, we probably wouldn't miss it: Arda is created, then we have endless war between the Valar and Melkor, then Melkor is chained and Eru's children enter. Works perfectly to me, no gap. What is special about the Second Theme is that, in the end, Melkor had the mastery. Sure, he did have mastery over Middle-earth from the raising of the Pelóri until his chaining, but I doubt this is enough to deserve a theme of its own.
I never regarded the Music as a sort of chronology, with each note symbolising some event. Horribly simplified, I see it as a 'manual' for world-builders. Eru shows its children how the world is going to be like. Now, this would mean that Melkor, for a time, has the mastery over the creation of the world. While his influence on the First Theme I imagine to have been more on the 'snowflake-level', his influence on the second was serious - and I can only think of the Marring in this respect.
What I wondered about is, Eru tells Melkor that nothing can be played that has not its source in him. This holds explicitly for Melkor's discords. Wouldn't this then mean that all the evil that Melkor brought into the world has its source in Ilúvatar, too? I mean, where else could it have come from if Melkor couldn't invent it himself? And if Melkor deserves punishment for his deeds, why doesn't Eru?
I hope I won't be stoned for this blasphemy...
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