To respond to your comments all at once, I want to suggest that the alchemical method, at least as Newton practiced it, incorporated all of the necessary elements that modern philosophers of science would recognize as good science.

Newton’s alchemy involved investigating empirical phenomena in the external world, meticulously recording their _reproducible_ transformations, and attempting to infer law-like patterns which tied together and might explain these observations. Like today’s modern physicists, they were very much interested in Theories of Everything which might tie together and explain widely disparate observations. Of course they embraced chemistry when atomic ratios were discovered. They were immediately able to recognize its value and explanatory power since they were committed to a particular methodology, but perhaps not any particular paradigmatic model of nature (other than its underlying unity).

Imagine observing this phenomena – http://www.pbs.org/wgbh/nova/newton/alch-newm-02.html – without Stephan Wolfram, fractal geometry, molecular and crystal theory, and about a half a dozen other modern day fields of math and materials science. Doesn’t strike me as shameful to postulate an “active principle” responsible for growth like this.

I think things get really interesting when you do view their discipline as an form of exegesis – their Theory of Everything incorporated and included meaning and consciousness, unlike many of the popular TOE’s floating around in today’s circles.

As for something the ancients knew that we have forgotten, or gotten all mixed up, what about the notion that information or consciousness is primary, and matter and energy supervenes on it instead of vice-versa? Something along the lines of http://en.wikipedia.org/wiki/Amit_Goswami or (Elements of Reality: A Dialogue. Piet Hut. Bas van Fraassen – http://www.google.com/search?q=cache:EJyVkrZ6MAYJ:www.ids.ias.edu/~piet/publ/elements/elements.ps+bas+van+fraassen+piet+hut+Elements+of+reality:+a+dialogue&hl=en&ct=clnk&cd=1&gl=us&client=firefox-a) which more and more respectable theoretical physicists and philosophers of science are beginning to explore.

1. The confluence of when Newton wrote the Principia Mathematica and other alchemical work hardly conjoins the quality of one to the other. An equally valid story is that he had descended into thinking about nonsense after coming up with the Calculus. Only the threat of Leibnitz and other scientists to publish ahead of Newton spurred him to write the PM.

2. Newton was not beyond error. In my personal academic career, it came up in PDE that Newton’s error in solving a PDE equation possibly retarded the invention of powered-flight by a century or two.

3. “Perhaps the ancients might have been on to something that modern science has truly forgotten.” is not something I’m implicitly averse to. I simply wait for your evidence. The industrial revolution–an apparent abandonment of alchemy has made the western pauper wealthier (and in some cases, even more powerful) than the royalty during Newton’s age. As a series of mnemonics, memory aids, and accoutrements to pre-chemistry, it seems to have held up. But alchemy was also responsible for ‘humour’ medicine–which created the rare historical moment when a wealthy person who could afford ‘doctors’ was more likely to die than those that could not afford ‘medicine.’ Those that used alchemy drifted pretty swiftly into chemistry when atomic/molecular ratios were discovered.

4. Personally, I’d rather view it as a form of exegesis–like Marxist or Freudian critical analysis. Just like those exegetical methods, it opens certain windows when applied to literature, but can have strange and even malfeasant results when applied to medicine/science.