He notes a claim in contemporary physics that, as far as I know, has gone unchallenged. Two theories in quantum mechanics, the "Böhm" and the "Copenhägen," have exactly the same experimental consequences but are nonetheless "radically different" theories. Each makes the same predictions about what is likely to happen, given initial conditions, thus fitting the data equally well. But the former is stochastic, i.e., it works random chance into its statistical calculations; whereas the latter posits that "events can instantaneously affect other events a vast distance away." The upshot is that
...the two theories share the same formalism - the same outer mathematical structure which is a way of making the theory formally correspond to the data of experiments - and yet they have very different interpretations, that is, understandings about how the world actually works. It isn't that any theory at all can match the data - that is, can share the same formalism. Obviously many theories exist which do not match the data. But in quantum mechanics more than one mutually incompatible theory exist which match the data perfectly, and the reason one is taken to be true (Copenhagen) is a matter of historical contingency; it isn't because Copenhagen comports with observation and Bohm doesn't.If, as in this case, more than one formalism yields the same successfully testable results, then reasons for preferring one over the other are metaphysical, not scientific. Such reasons are consistent with the science but not necessitated by it. Nobody disputes that. But why is such an arcane fact from a discipline that is beyond most people pertinent to religion?
Consider the standard, neo-Darwinian theory of evolution: that the origin of species can be explained purely as the result of "natural selection," i.e., random genetic variations that survive, or do not survive, according to their relative reproductive success or failure. Is that theory a "formalism," in the sense that, by plugging in the relevant data, we can be told "in a fully generalizable way how reality will behave?" No, it is not. That doesn't make the theory of evolution false, of course; but it cannot be formalized in such a way as to make predictions according to which the same results will always be got out of the same data. Thus the theory is partly an "interpretation," not a "formalism" as are the theories of physics. And that in turn means that the data do not, just by themselves, show that the theory can be generalized to explain everything about the emergence of life in general and species in particular. There might be good reasons for preferring such a theory to its competitors, but those reasons are not scientific reasons and are not ironclad. They are metaphysical—to use a word that is as embarassing to many scientists as would be showing up to a prom in their underwear.
That Darwinianism is partly metaphysical ought not to be controversial, but it is. Scientists do of course proceed on the basis of what's called methodological naturalism, the thesis that, in looking to explain physical realities, we should seek only natural not supernatural causes. There is nothing wrong with that; in fact, to do otherwise would not be science, as that form of inquiry has been so successfully practiced for centuries. But methodological naturalism does not logically entail metaphysical naturalism: the thesis that Nature is all there is. Neither, therefore, does it entail scientism: the thesis that what can be known by purely scientific means is all there is to know. Methodological naturalism is simply science; metaphysical naturalism is—well, metaphysics, and scientism is its epistemology.
That's not to endorse "intelligent design" as science. ID is metaphysics too. It can no more be verified scientifically than metaphysical naturalism. Thus Darwinianism and ID should not be seen as scientific competitors. Both are consistent with the data. But the value of ID is that it points us to another fact that ought to be obvious: explanations of reality can be and typically are layered.
Suppose somebody asks you why a pile of wood is burning in your yard. You then proceed to explain the physics of combustion. But back comes the retort: "I know all that; I wanted to know why you are burning a pile of wood in your yard." You haven't gotten the point of the question; it's after a purpose, not a mechanism. The answer might be that you could think of no better way to prevent termite infestation, given that you failed to use all the wood last winter for firewood. Or it might cite some other purpose. But whatever the purpose, the mechanism of combustion remains the same. The mechanistic and purposive explanations are not only compatible; the former is layered within the latter.
For all that "science" tells us, the same might be true of the universe in general. After all the strictly physical explanations of events are given, the question "Why?" remains. It either has or doesn't have an answer in terms of a purpose. If it does, then the science tells us something about how the purpose is embodied. If it does not, then what the science tells us is all there is to tell. But in either case, the science remains the same.
That should offend neither scientists nor theists. Nobody need worry about turning up at the science prom in their underwear. That's for a different venue.