Well, it's been pointed out on occasion that modern physics did get back to alchemy - in the sense of transmuting elements (radioactivity). Personally, I took Root as referring to what the alchemists did achieve: apparent immortality, given his presence in Cryptonomicon. The younger order achieved a great deal, but just as map projections always have difficulties caused by mapping 3D to 2D, the younger order has difficulties with a few singular parts of the territory, if you will.