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Dear Christi,
your essay was an interesting read. I think your realization that ultimately, all we know of the world are relations is very deep, and is in a certain sense at the foundation of my own thinking, as well. However, I am less certain about the 'book containing every truth': this seems to me to run into trouble with the Kochen-Specker theorem (and related ones). In particular, if such a book existed, it would imply the existence of a global probability distribution such that its marginals give the outcomes for every possible set of observations; but this is known to be at variance with quantum mechanics. Put differently, while classically we can identify every object with a list of properties, of propositions true about this object, in quantum mechanics, no such list can exist. Any theory for which such a list exists necessarily obeys Bell's inequalities (and Kochen-Specker and Leggett-Garg inequalities, which are from this point of view just variations on a theme). (I think this connection was probably first worked out by Fine.)
Nevertheless, your big book seems to be very much a 'hot idea' in philosophy at the moment, after having been somewhat maligned after the 'noble failure' of Carnap's "Der Logische Aufbau der Welt"; three books have appeared in the past year dealing in various ways with the possibility of deriving all truths about the universe from some 'compact class' of basic truths: David Chalmers' "Constructing the World" (which is the only one I've read... well, I should say 'almost read'), Theodore Siders' "Writing the Book of the World", and John Heil's "The Universe as we Find It", so you're certainly at the bleeding edge in that respect! (Just in case you're interested.)
In any case, as a fellow PhD student in physics, I wanted to emphasize one point you made, though only somewhat implicitly, and only tangentially related to the main thrust of your essay: that of the necessity for courage in the scientific endeavour. Building on the Kuhnian model of scientific revolution, one might say that the ordinary, stick-to-the-mainstream method of science fails to produce the most important new ideas: it only clusters around local maxima, so to speak. For true innovation, one must sometimes leap beyond what seems reasonable, or even sensible within the current paradigm. Of course, many, if not most, such leaps will lead to nothing, which is why one needs courage to make them---a courage which John Wheeler certainly possessed, as you have shown in your essay.