I'll not get into most of the theological stuff the thread has become, since it doesn't particularly interest me. Da Vinci's religion, however, is NOT something you can clearly and completely claim.
Personally, if I was going to make a guess at his belief system, I would tag him as a theist, who seemed to believe in a non-interventionist God, but I'll be honest enough to admit that is a guess based on very sketchy evidence.
A few things on this;
1) You are correct in that Vasari commented on his cast of mind being heretical, and that this notation was removed was the subsequent edition of the text. I am personally unaware of a definitive cause for this removal, and believe it's conjecture as to why it was removed. 'He admitted he was wrong' would indicate you have some knowledge of this I don't, I guess?
2) He painted Christianity's greatest works. Sure. Not for free though. It was on commission. How this proves his piety is beyond me. The church was an inescapable fact of life in his day (even if he cared to escape it...as I said, I'm not claiming him as anything)
3) It's pretty easy to claim people as Christian in a time when Christian worship wasn't just the norm, but demanded. The man was intelligent, not suicidal.
IN his own words (extract from his notes)
"I am well aware that because I did not study the ancients, some foolish men will accuse me of being uneducated. They will say that because I did not learn from their schoolbooks, I am unqualified to express an opinion. But I would reply that my conclusions are drawn from firsthand experience, unlike the scholars who only believe what they read in books written by others."
"Although I cannot quote from authors in the same way they do, I shall rely on a much worthier thing, actual experience, which is the only thing that could ever have properly guided the men that they learn from."
"These scholars strut around in a pompous way, without any thoughts of their own, equipped only with the thoughts of others, and they want to stop me from having my own thoughts. And if they despise me for being an inventor, then how much more should they be despised for not being inventors but followers and reciters of the works of others."
"When the followers and reciters of the works of others are compared to those who are inventors and interpreters between Nature and man, it is as though they are non-existent mirror images of some original. Given that it is only by chance that we are invested with human form, I might think of them as being a herd of animals."
"Those who try to censor knowledge do harm to both knowledge and love, because love is the offspring of knowledge, and the passion of love grows in proportion to the certainty of knowledge. The more we know about nature, the more we can be certain of what we know, and so the more love we can feel for nature as a whole."
"Of what use are those who try to restrict what we know to only those things that are easy to comprehend, often because they themselves are not inclined to learn more about a particular subject, like the subject of the human body."
"And yet they want to comprehend the mind of God, talking about it as though they had already dissected it into parts. Still they remain unaware of their own bodies, of the realities of their surroundings, and even unaware of their own stupidity."
"Along with the scholars, they despise the mathematical sciences, which are the only true sources of information about those things which they claim to know so much about. Instead they talk about miracles and write about things that nobody could ever know, things that cannot be proven by any evidence in nature."
"It seems to me that all studies are vain and full of errors unless they are based on experience and can be tested by experiment, in other words, they can be demonstrated to our senses. For if we are doubtful of what our senses perceive then how much more doubtful should we be of things that our senses cannot perceive, like the nature of God and the soul and other such things over which there are endless disputes and controversies."
"Wherever there is no true science and no certainty of knowledge, there will be conflicting speculations and quarrels. However, whenever things are proven by scientific demonstration and known for certain, then all quarreling will cease. And if controversy should ever arise again, then our first conclusions must have been questionable."
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The only other thing I wanted to mention in relation to this thread is that whether or not you believe Muhammad is a prophet (and I obviously do NOT), he is a historical figure of note. Assume he is a false prophet and still look at the political change he wrought in the Middle East. The impact this had on the Roman Empire alone is enormous.