(I can see that this is going to be tough going as fiction, as Chris says -- and probably not worth the effort - for me, at least. But I'll let the "initial comment" below stand, and put this book back on the shelf. The Author's Note at the back of the book is worth reading.)
In the notes appended to the english edition of Memoirs of Hadrian, Youcenar writes to Frick that the book was in large part inspired by a quote she found in 1927, from Flaubert's correspondence, that runs: "Just when the gods had ceased to be, and the Christ had not yet come, there was a unique moment in history, between Cicero and Marcus Aurelius, when man stood alone." Thus, the whole of the Hadrian book is a meditation and celebration of the classical pagan humanism (for the nature of which, see also Cochrane's famous Christianity and Classical Culture: http://www.goodreads.com/book/show/637473.Christianity_and_Classical_Culture).
The Abyss starts with a quotation (in the motto) from Pico della Mirandola's Oratio de hominis dignitate that runs (in part): "I have given you, O Adam, no fixed abode, no visage of your own, nor any special gift, in order that whatever place or aspect or talents you yourself will have desired, you may have and possess them wholly in accord with your desire and your own decision. Other species are confined to a prescribed nature under laws of my making. No limits have been imposed upon you, however; you determine your nature by your own free will...." -- a passage which finds its direct echo in J.-J. Rousseau's Second Discourse, where Rousseau argues for the plasticity of man -- the central premise underlying Rousseau's humanism.
Zeno -- the chief character in The Abyss -- is placed (in the middle of the 16th century) at the crossroad where the Medieval worldview (essentially Aristotelian) was giving way to Modernity and early modern science -- to Bruno, Brahe, Copernicus, Galileo, and (ultimately) to the great Descartes himself. For this junction, see the classic treatments of Koyré and Burtt, two magnificent books.
(With books like this, ignore the the fact that there are some people give these books two or three stars... People who do this are simply ignorant. These are must read books.).
But the birth of modern science was not simply the birth of a mechanistic system -- because modern humanism -- and this line runs from Rousseau to Marx and to Freud --, while materialistic, is not mechancistic -- but contains an element of vitalism (there is no 'spirit'; everything is matter; but matter is alive -- "thinking matter", in Yolton's phrase. This is a line of thought that traces back to the Stoics, and of course survives in the thought, for example, of Alfred North Whitehead (Science and the Modern World). It is key to understanding the humanist interpretation of Marx that was first espoused by Rodolfo Mondolfo.
But what is interesting here - and why I mention all this in the present context -- is that Yourcenar (quite accurately) traces this vitalistic element to late renaissance alchemy. She writes in the author's note (p. 364f.): "On a purely intellectual level, the Zeno of this novel, still marked by scholasticism, though reacting against it, stands halfway between the subversive dynamism of the alchemists [Y. is thinking here of the likes of Paracelsus] and the mechanistic philosophy which is to prevail in the immediate future, between hermetic beliefs which postulate a God immanent in all things [again, think Giordano Bruno; and see Koyré] and an atheism barely avowed.... Such a position is not unique in this century [16th]".
Regardless of how this book turns out from a novelistic point of view, Yourcenar's grasp of intellectual history is profound and reliable.