Robert Boyle - The Sceptical Chymist
Robert Boyle was born in Ireland as the seventh son of the Earl of Cork.  He was educated at Eton after extensive travel he became acquainted with Samuel Hartlib and his circle of friends in 1650.   This group referred to themselves as the 'invisible college'.  The Hartlibians were interested in exploiting chemistry both for its material usefulness in medicine and trade and for the better understanding of God and Nature.    The group included the American alchemist George Starkey and Robert Boyle began to read extensively into the alchemical literature. Between 1655 and 1659 and from 1664 to 1668 Boyle lived in Oxford, where he became associated with the group of talented natural philosophers who were to form the Royal Society in 1661.

Boyle was a extremely devout man who, like Newton, wrote as much on theology as on natural philosophy.  He paid for translations of the Bible into Malay, Turkish, Welsh and Irish, and left money for an endowment for annual sermons that where to reconcile and demonstrate how science supported religion.


A two jet Hero's Engine
The generation before had seen a revival in the fortunes of the atomic theory of matter.  In 1575 Hero's Pneumatica (62 AD)  was found, published and disseminated an alternative non-Epicurean atomic theory in which the properties of bulk matter were explained by the presence of small vacua that were interspersed between the particles of the body. 
This theory, which allowed heat to be explained in terms of the agitation of particles, as exploited by, among others, Galileo, Bacon and Helmont in their search for an alternative to Aristotleanism. In 1660 a French philosopher, Pierre Gassendi  advocated the Epicurean philosophy of atoms to replace Aristotlean physics. His work also advocated a vacuum between atoms which provided an alternative to Descartes' plenistic particle theory. 
    Pierre Gassendi
René Descartes
Descartes' three grades of matter, i.e. large terrestrial matter, more subtle or celestial matter that filled the interstices of the former, and still subtler particles that filled the final spaces, bore more a passing resemblance to the elements of earth, air and fire, let alone Paracelsus' principles of salt, mercury and sulphur.  To these men above Boyle was much indebted.  He also owed gratitude to Walter Charlton, whose Epicuro - Gassendo - Charletoniana (1654) had not only presented a coherent mechanical philosophy in terms of atoms or corpuscles, but had placed it in an acceptable Christian context.

In 1661 Boyle published 'The Sceptical Chymist', a critique of Aristotlean, Paracelsian and Helmontian chemistry and the substantiation of physical and chemical properties.  The book was designed as a argumentative discussion amongst four scholars.  One was a skeptic, one an Aristotlean, one a Paracelsian and the last a neutral.
Instead of going through the entire treatise let's summarize the main points.

1)    Of the four-element theory, the most common experiment was the burning of a green-stick.  this was supposedly proof of Air, Water, Fire and Earth.   Boyle raised the following objection:  Although all matter consists of the four types, is it possible to extract more or fewer?  "Out of some bodies, four elements cannot be extracted, such as gold, out of which not so many as any one of them has been done up to now.  The like may be said of Silver, salt and diverse other fixed compounds.  Extracting any of these substances has proven to a task even Vulcan cannot do...." (I paraphrased greatly here.)

2)   Of the four elements, Air, Earth, Fire and Water he objected to the fact that these were considered to be elements at all.  "As for the green stick, the fire does not separate it into element s, but into more mixtures, disguised in other shapes. The flame seems to be tainted with sulphur and the water boiling from the end contains salt and the same minerals as in concrete.  The smoke is so far from being air, that it should be considered a mixture which can itself be distilled yielding an oil and an earth behind.  The earth abounds in a salt that when mixed with water makes an irritant that causes the eyes to water unlike the smoke from pure water.  From the water salt mixture a pure white, volatile and penetrating salt can be extracted"  (Again I paraphrased drastically here...)

The criticism clearly shows Boyle's careful analysis of the destructive distillation of wood.

3)    Finally, Boyle turned his criticism on Fire analysis itself. Why was it he asked that if the conditions of fire analysis were slightly altered ot a different method of analysis was used, the products of analysis were different?  Thus if a Guajacum log was burned on an open grate, ashes and soot resulted; but if distilled in a retort, you got oil, spirit, vinegar and charcoal?  And whereas 'aqua fortis'  (concentrated nitric acid) separated silver and gold by dissolving the silver, fire on the contrary, fuse the two metals together.  Moreover the degree of fire (the temperature) could make the results of the analysis different.

Boyle stated that the use of logic and philosophy were highly suspicious when investigating matter.  True experiments should be based measurable values and observation, and not conjecture and a desire to make the results fit the theory.  The theory should be changed to fit the experimental results.