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Eliezer,
You're ignoring the logic of evolution. When Feynman looked at the wine glass and saw the whole universe implied therein, he was of course looking through the lens of physics. Further, he was, I think, making two distinct observations.
First, the greater part of what we actually know about the universe is reflected in the behavior of that glass and its content. That is you take all the concise formula of which we so far know then some part of the behavior of the wine glass will show evidence of most of those formula either directly or by artifact.
Second, there are still a great many things about the behavior or the nature of that wine glass that we do not understand. If we understood all the mysteries, extracted all the formula, then a major hunk of the rest of the universe would suddenly become clear.
It's that second point that is at the root of my queaziness about your judgement of others for their irrational beliefs. For the reality is that logic and the scientific method will only take one so far. Most of the world we live in we do not understand. Most of it. Most of the things -- unfactored by even a proper name -- that affect you and me and determine the quality or even the existence of our lives are not understood and certainly show no immediate prospect of becoming comprehensible.
So what do we do with all this vast darkness that figuratively surrounds us on all sides? Naturally we focus on what we do understand: the fire. But the darkness is still there and we have to somehow deal with it.
We deal with it by guessing. Or by believing what we prefer to believe. Or by believing the same things that our parents believed. The virtue in these things is not that they are correct; because they are almost certainly not, but instead that people believing similar things have repeatedly survived. The only logical screening here is the evolutionary one. Some beliefs are fatally wrong. This is not to say that people don't continually rediscover fatally wrong ideas but the tendency is simply because we are the descendents of the survivors to not adopt beliefs that leave no children behind.
Thus you are looking at these irrational beliefs through the wrong lens. They are not really about truth. They are about beliefs that help people to survive.