The Pope of Literature
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Chapter Three: Realms of the Spirit
1. I disagree that it's "not difficult to understand how human beings first came up with the idea" of a spirit associated with living creatures. Our familiarity with the concept tends to mask just how novel and radical an idea it must have been. Why would ancient people have decided that the seat of the personality was something that escaped from the body at regular intervals? Moreover, what surprises us about many primitive societies is not the naivite of their thought, but its sophistication. And the elements that strike us as naive seem more often than not to have developed alongside of, if not after, the developments that startle us with their sophistication. Thus, religious conceptions associated with iron, meteors and the crucible do not seem to have preceded the development of metallurgy. I'd say it's entirely unlikely that the idea of the spirit was the result of any form of crude evidentiary method -- in other words, our ancestors likely did not conceive of the spirit because they didn't understand the phenomenon they witnessed, but because their familiarity with those phenomenon made them useful as symbols for something else.
2. As a matter of historical clarification, it was the philosophers and scientists responsible for developing modern scientific method who deliminated it such that "the realms of the spirit" were off-limits to its method. They did so, in fact, in order to keep religious speculation out of scientific inquiry, and to circumvent any attempts to explain natural phenomenon by reference to a divine order. Hume, for one, was instrumental in demarcating the territory of science; Descartes, as well. I'm not sure that Voltaire actually added anything substantive to scientific method, but his work also contributed to the formation of a methodology that set aside a priori any non-material claim. A lot of modern scientific critics of religion (again: Dennett, for instance) seem to demand the benefits of that demarcation without accepting the limitations it implies. But those limitations are the direct logical consequence of the very deliberately developed nature of scientific method.
3. While we're at it, the natural/supernatural dichotomy is also, as best as I can tell, a fairly recent concept, an adaptation of neo-Platonic ideas forwarded by Enlightenment rationalists who wanted to compartmentalize religious thought enough to make it possible to ignore altogether. The adoption of that dichotomy among religious groups seems to have been a more gradual process and, from their perspective, an unfortunate one. Any time one group adopts a term intended by another group to polemicize a topic, they open themselves to all sorts of criticisms that wouldn't have been available otherwise. And the more they buy into the terminology of that polemic, they more likely that are to restructure their own thought in ways that make them even more susceptible to criticism. It seems entirely likely that, prior to the Enlightenment, most Christians conceived of the universe as an Aristotelian unity, wherein the divine pantheon was part of the natural order. There was no supernatural realm to speak of, and with that conception, it was still possible for orthodox Christians to cognize science as a legitimate tool mandated by God for understanding the natural world. There's plenty of historical evidence to suggest that this was the case. What seems to have happened in the meantime is that the natural/supernatural dichotomy has set the stage for a social schism over the value of science in relation to religious belief, whereas, without that dichotomy, modern Christianity might have made a more earnest attempt to reconcile scientific inquiry with religious doctrine, and vice-versa.
4. Incidentally, all the talk of bamboozling and "the perfect con" -- you seem to be drifting even further from you stated goal of talking about religion and atheism "in a way that is neither patronizing nor elitist."
5. And on the subject of reason and the irrational, I can understand your bewilderment. The debate between the rational and irrational impulse is one that seems odd outside of its historical context, and our society has largely lost sight of that context, despite the fact that some of the best statements of the problem were made within memory of many still living. (I'm thinking specifically of T.S. Eliot's "The Wasteland" and George Steiner's "In Bluebeard's Castle".) As late as the 17th century, Reason was still a concept dear to the Christian heart. But at some point during the Enlightenment, reason became something of a polemical term, a way of compelling agreement and cooperation by asserting the your position was more objectively valid. Once reason was established as the sort of problem-solving that should be possible for any normally functioning person, it became equally possible to argue that, so long as your solution was rational, there was no impediment to imposing it on others because, after all, given all the facts, they'd have come to the same conclusion.
A fair starting point is the prominant place given to reason in the French Revolution -- you can take that language literally, since during the Revolution a ceremony was held in which a woman dressed as Reason personified was feted and crowned in Notre Dame cathedral. (Carl Becker, "The Heavenly City of the Eighteenth Century Philosophes") But the Revolution was violent, disruptive affair, and its results have not been entirely well-regarded, even by those who were its putative benefactors. Another major stage was the rise of the industrial revolution, and the rise of the industrial factory system was accompanied with a great deal of propaganga to the effect that even the pisspoor living conditions of the workers in factory towns was a commendable application of Reason to the problems of economics and social control, and that the inevitable result was Progress (Dickens' "Hard Times" is vivid illustration of that theme). In terms of Western intellectual development, the culmination and breaking point for this dialectic of reason came with the first World War, the much vaunted "war to end all wars". What it ended was the optimism and faith of all the intelligensia unfortunate enough to get involved, and the body of literature produced by veterans like Robert Graves, Sigfried Sassoon and the much anthologized poets of WWI England did much to forward a criticism of modernity. (Paul Fussell, "The Great War and Modern Memory") The calculations of the second World War intensified that scrutiny -- whereas the rational application of science had previously produced the machine gun and the tank, it now produced the gas chamber, Nazi human experimentation, and atomic warfare. All of these were initially presented as solutions arrived at by the judicious application of reason to the problems of modern warfare, and the voices of those opposed were still largely by those in authority by an appeal to reason.
Naturally, reason on its own doesn't produce those things, but then, understood in its proper context, the criticism of Reason is not a criticism of the faculty itself. It is, at base, a criticism of the polemics that attend it, of the assertion that, because a given policy or technology represents the deliberate application of reason to a specific problem, any debate on the matter is patently absurd, counter-productive, anti-social, etc. There is in such debate an attempt to remind those with influence and in authority of the dangers of abstractly applying reason to a problem without bearing in mind that the solutions will effect actual humans, whose well-being and happiness is often contingent on factors not dictated by or included in rational consideration. It serves as a reminder that our moral objections are not always obviously as rational as the policy that concerns us, and that, ultimately, morality is built on premises that are not entirely reducible to logical argument. It's also a reminder of the severe limitations placed on our ability to encompass enough information to make truly informed policy. And in some ways, it's merely an objection to the use of the phrase "be reasonable" as a discussion-stopper.