By far the most common mistake over the last hundred years in the teaching of the history of science and the evolution of scientific ideas frequently also made in the teaching of the processes of biological evolution is to falsely impart a clear-cut narrative with good guys, bad guys, winners, and losers. The story of the heroic emergence of chemistry out of the Middle Ages' supposedly silly and irrational approaches to natural science is an example of this problematic tendency. Certainly, to a modern reader, the physical theories of the Scholastics seem thoroughly absurd, but upon examination of the data actually available to would-be scientists of the day, the set of ideas is nearly as self-consistent as the modern scientific paradigm; it fails only in consideration of the real information not available until well into the modern period.
The idea of memes', transmissible patterns of thought or units of cultural information, is useful in the understanding of how profoundly researchers' approach to the physical world before the mid-1700s differed from that which prevailed in subsequent centuries. From the perspective given by memetic theory, that classic example of unscientific medieval foolishness, the idea of the transmutation of metals, is entirely consistent with the best information, theory, and accepted scientific philosophy of the day.
The first point to consider is that the analytic methods available to the medieval and early modern natural philosophers who believed in the reality of transmutation of metals can scarcely be compared to those presently available. Almost everything modern chemists take for granted consistent and clean instruments, constant heating elements, airtight seals, sometimes even transparent glass were either nonstandard or completely impossible to achieve. Small wonder, then, that things like escaping gas were not understood and incorporated into the physical model of the universe.
Secondly, the historical spectator must consider the period's different attitude toward the nature of the universe and of the possibilities of human endeavour. The period we call the Enlightenment bequeathed a meme to the Western world that mandated a strong separation between the realms of unverifiable theological and philosophical speculation on the one hand, and on the other hand concrete and testable scientific discovery. However, to the Medievals this was not the case. Instead, everything in the world was intimately intertwined with theology, in the sense that everything was specifically designed by God, as in the poem by Alain de Lille:
Omnis mundi creatura
Quasi liber et pictura
Nobis est in speculum
- that is to say, every living thing was a book or a picture in which to see the play of existence acted out by man as God intended to see the life, fortune, and death of humanity as if in a mirror. This close association between the physical and the metaphysical imparted a very different understanding of the aims of natural philosophy. In addition to this, the importance of experimental verification and reproducibility were not part of the memeplex associated at the time with chymistry. Thus, nearly all the standard memes associated with what we now call "scientific inquiry" were not at that time important in the understanding of the natural world as they saw it.
The theoretical basis for understanding physical processes was correspondingly different, too, of course. Although it evolved and changed somewhat through the centuries, the basic theory of matter remained relatively consistent throughout the medieval and early modern periods. The sulfur/mercury theory, with the six metals and assorted other theoretical constructs, did a reasonably good job of explaining the observed phenomena, as reading either the cryptic texts of the Middle Ages or the elaborate lab notes of Boyle and the other Early Modern experimentalists will reveal. In addition, it accomplished a task which no modern chymist would ask of it it explained not only the changes of earthly objects and the motions of the bodies in the heavens, but attempted to connect all these ideas to God's great Plan. It seems likely that physical understanding is somewhat impeded if one requires that one's physical theory also attempts to explain the mind of God. Given that they did require this, though, and given the difficulties in method with which they had to contend, the Aristotelian elemental view of matter and consequent embrace of transmutation was a self-consistent and reasonably explanatory physical model.