Plato* makes it clear his system is distinct from natural science, and in some sense opposed to it, since sciences reduce to fundamental integral parts while Plato reduces to form and therefore also, in a different sense, to the teleological causality of mind. Plato’s system has costs, of course: even Plato is clear that his own approach has a sort of simple-mindedness that science has no patience for, since explaining by form often amounts to saying things are bigger by bigness, hot by heat, alive by life (or “soul”) etc.
For all that, forms exist and so overlooking them leaves some things inexplicable. The “hard problem of consciousness”, for example, is what knowledge or consciousness adds to mere physical information or encoding, but what it adds is a different ratio or esse of form, i.e. form as intentional or ordered to knowledge. So long as form is left out of the discussion consciousness will always be illusory or irrelevant. No matter how precise, useful and predictive our scientific accounts of knowledge get, they’ll involve an explanation where an addition to physical and encoded information is superfluous.
There is a similar “big problem” about the universe – as Hawking put it: “Why does the universe bother to exist?” The problem is insoluble from within science since existence is not just form but the forma formarum. Existence is most of all what we mean by form, relative to which other forms are not so much beings as ordered to being.
In the absence of form it becomes impossible to give any principled division between physics, chemistry, and biology. The living is divided from the non-living by form, and the non-living divides into the absolutely simple and the complex molecular by another formal division, with chemists seeking to reduce the complex to the simple and physicists seeking the simple absolutely. Given only science, no one can figure out why one would ever divide these sciences from any principle intrinsic to them, but as soon as one sees that the fundamental inanimate, complex inanimate, and the animate are three orders differing by form, the reason for their division is obvious and unavoidable.
The inability to give a principled distinction between the animate and inanimate will arise in part from an inability to see the distinction between the natural and artificial orders, since this too reduces to nature having an intrinsic principle whereas the artificial, even at its most complex, (the machine) does not. It’s from this that the sciences have their peculiar disposition to atheism, for it’s the forms in things that are most of all what are divine in them, and whose intrinsic powers of operation are always taken for granted in human art. Said more simply, overlooking form leaves no principle for dividing human art and divine art in kind.
Because form is the principle of operation, the sciences cannot give a primary source of operation or action, but will always chase it back either infinitely or to a beginning that is only such accidentally or by fiat. Sciences always take up the story of an action in medias res, so the causal story they tell is on the one hand deterministic or random (depending on what your theory of laws is) and on the other hand homogeneous with no essential first principle. No cosmological argument is possible in scientific terms, except accidentally, and even this accidental theistic argument gives one no scientific resources to describe its cause as divine.
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*As accepting the reality and causality of form, of course, “Plato” is Aristotle is Neoplatonism is the whole of Scholasticism, notwithstanding their violent diversity. Still, all the points in the first paragraph are Plato’s in his argument against Kebes in Phaedo.