I note that the interpretation that I have of Ainulindalë is extremely different at a fundamental level than yours. From what I understand, the Music creates all of the elements of the (admittedly first) conception Arda,
all of them, including Elves and Men. But the Valar do not understand how it works in its entirety; they only understand those portions of the Music that pertain to them. This is why the Valar all seem to have elemental or other affinities, Varda with light, Manwë with air, Ulmo with water, Aulë with fire, Yavanna with earth, Melkor with darkness, and others that are less obviously elemental. Contained within the Music is the power that makes Elves and Men, something which
none of the Valar understand, which is why they seem able to act beyond the Valar. I agree with you that Men in particular are singled out as having an unspecified destiny, that they can control fate.
As for Arda Marred and Arda Healed, I see Arda as an object in four, even five, dimensions, which is, I think, how Ilúvitar Himself would "see" it. We know in Ainulindalë that Ilúvitar's halls are "timeless". We may presume that time (as we know it) does not pass within them; obviously there still is some level of cause and effect, but it would be "meta-time", not Time in Arda. This means that, to one who knows or sees the Music, Arda is visible in its entirety, both in space and in time. Yet, somehow, souls are not part of Arda, why they can participate in the Second Music, something that will in the next frame meta-time will "heal" Arda. In reality it will mean Arda Remade, and Arda Marred will become Arda Unmade.
I dislike having Ilúvitar directly intervene in the workings of Arda for this (and other) reasons. Ilúvitar is, to my mind, understood to be all-knowing and all-powerful. Why should He have to alter anything? All He needs to do is let his plan (which is, of course, perfect) unfold. If Ilúvitar did decide to make a change, nobody on Arda save the Valar would notice: it was a change in the Music, which means a change to the past as well as the present, so to anybody it would be as though it had always been that way. The only reason why the Valar would notice is because They saw the Vision and the Music before entering into it, so They might notice a change from the original, assuming that They recognized enough of the Music to notice it!
Speaking of which, this explains a problem that comes up regarding the Changing of the World. In a letter, Tolkien noted that if anybody had stood upon the mountains above Lindon and watched the Elven ships sailing into the West, they would have noticed the ship simply getting smaller and not experiencing an effect of "hull down", when a ship sinks over the horizon. The reason why this phenomenon occurs is of course due to the fact that the Earth is a sphere, and that the observer's view is being obstructed by a curved surface. Yet, in Unfinished Tales, there is mention of Númenorean sailors observing the peak of the Meneltarma being visible before they see the lower parts of their island, indicating that they, too, were sailing on a curved surface, not a flat one like Arda Unchanged was supposed to be. I suggest that the reason why anybody knows about the Changing of the World is that enough of the underlying plan for Arda was known that it was originally "meant" to be flat, and that the downfall of Númenor had something to do with its not being flat, despite the fact that it was a sphere even while Númenor was still there!
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In any case, what Tolkien was writing was a myth.. and myths that include a "Genesis" story definitely need to have such conceptions as "soul" and "afterlife" explained in my opinion.
This may not actually true: the ancient Sumerians did not, I am to understand, believe in an afterlife. There is next to no mention of an afterlife through much of the Old Testament as well (including the book of Genesis itself). I think that the importance of the afterlife to modern religion is something that was added later - although it was certainly added independently a number of times.
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I'm afraid I can't say I agree with this one either. I don't think there ever was an intention to make the death of Men something different than it is in our world – and yes, for Tolkien as a Catholic, it definitely involved an afterlife of sorts. He may not have written it down in his first stories, but there is nothing to indicate he "changed his mind about the spiritual state of Men" at any point.
The only evidence to imply that Tolkien "changed his mind" is the existence of ghosts in his stories, since ghosts should not be possible given the account presented in the Silmarillion. I don't think he ever
really changed his mind, since he always was a Catholic. I think that the biggest change is that he actually started to think critically about the nature of Men in his stories!
My problem with Tolkien's blending of his religion with his legendarium is this: if human beings are immortal (which they are, if they have immortal souls, and that soul is the primary mode of a person's existence), then why should humans fear death? In particular, this is literature, and it is fantasy, heroic fantasy, in which heroes are trying to save populations from dying. Why should the
reader care, if the people getting saved are already immortal?
Obviously, the problem is solved if the focus of the theology is moved from the
fëa to the
hröa, since the
hröa is absolutely not immortal, not even for Elves (since they can still die of injury, just not of age). The obvious focus of Tolkien's published works is on the physical world with occasional hints at a spiritual one, and I think that is for a very good reason. I also know from a letter that Tolkien did not publish some of his later works because of its conflict with good storytelling.
This is, incidentally, intimately tied up with the Lúthien situation. As the link that you provided to the Council of Elrond discussion remarks, Lúthien is possibly
the most powerful of all of the Elven mages (you know what I mean) in the history of Arda, being
at least equal to Fëanor himself. Moreover, since the Silmarils contain the last of the Light of the Trees, they presumably have the last of Varda's power, of Hope, so as long as Melkor has all three of them, even the Valar cannot dethrone him. In short, Lúthien (and Beren) saved Arda. And they could do it again, if they were still
in Arda. This is why I like the Book of Lost Tales version of the story best; in it, it is possible that the two of them
will be coming back. In versions in which they won't be (including even the song that Aragorn sings in FotR, which is admittedly a legend told by those who don't necessarily know), there is the problem that a great deal of the subsequent decay of Arda could probably have been prevented by the two of them popping up at the right time and place. Now, if their primary existence is
bodily, then they won't come back anyway. Even if their spirits come back, they will be different people because they have different bodies. However, if spirits are the main deal, then sending their spirits beyond means one of two things: either (1) Ilúvitar (since He told Manwë what to do) is either callous, not really caring about all the bad things that will happen to Arda before Frodo and Sam do their job, or (2) Arda really is only a sideshow, and the place where B&L are going is the main attraction. I think we can rule (1) out, and if (2) is the case, then Arda is uninteresting: I want to know what the
real deal is!
(I also think that this is much of the reason why I am not Christian myself: I find its dogma jarring to my suspension of disbelief)
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I don't see the LotR really contrasting Tolkien's later (or earlier) conceptions of afterlife. I still don't agree with the spirits of the Dead Marshes being spirits of Elves or Men. Among the spirits haunting the Marshes there might be spirits of fallen Orcs, but Men – no. Also, we know that the Barrow-wights were sent to Barrow-downs by the Witch-king and they were NOT the spirits of those kings whose tombs they inhabited.
All of this is, of course, true, except possibly for the Dead Marshes sequence. However, these ghosts do contain
memories of the lives of the people whose graves they are haunting. I interpret this to mean that the dead left something behind. Of course, their souls, their
fëar, were
not left behind. This is why I am postulating the existence of yet another kind of spirit that people in Arda possess, that
could have been left behind.
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Beren, even if it might seem that I disagree with you a lot. It's interesting to see how other people interpret Tolkien's work and hear their explanations for it, especially if it differs from one's own point of view. There is no "right explanation" for anything and neither one of us is "wrong." Heck, the professor contradicts himself already often enough to have a fight with himself!
Speaking of religion, now you're preaching to the choir!

Indeed, if even the Professor argued with himself, surely I am free to argue with him, too!