In chemistry you have mundane chemical reactions whereas in Alchemy you have radical transformation. In chemistry the reactions are by and large fast but in Alchemy the transformations are slow. It is the honor of The Philosopher to repeat the processes earnestly, be it slow as they are, and enough times, until the processes occur in quick succession. In this way The Philosopher produces his stone, which can effect the slow degradations and reformations of Natural Order in a timely sense of fashion. To do this, The Philosopher must perform an allegory.
It has been speculated that Alchemy was of a purely psychological nature, and no processes were ever performed. However, Alchemy must bring to marry together both form and function. It must perform an allegory, making a physical mechanism of just thought. This means that processes in the physical realm dictate and correlate to a process going on within the individual. This connection of physical and mental allows The Alchemist to achieve The Great Work. This means that Alchemy reaches not just into the properties, but The Spirit of Matter.
Philosophy differs from spirituality and Christianity in that, in these, one must have the crucified individual, A Christ, to speak to the ultimate power through. Whereas in Alchemy, The Philosopher himself actually uses The Crucible, and in many cases as much. The Alchemist becomes the center of a perfect world, where he sets the order to it. As such, The Alchemist does not turn Lead into Gold strictly for commerce, but to prove that this world exists.