The naturalism that science adopts is
methodological
naturalism. It does not assume that nature is all there is; it merely
notes that nature is the only objective standard we have.
Supernaturalism is not ruled out a priori; it is left out because it
has never been reliably observed. There are many scientists who use
naturalism but who believe in more than nature.
Evolution does not in any way rule out the possibility of any outside
influence, even divine influence. When evidence for outside influence
has been observed, it has been included.
Science does not include anything that leaves no evidence that might
be tested. Hypotheses that can be asserted but never supported are
not part of science. However, these untestable phenomena are only
removed from scientific consideration; they are not ruled out from life
entirely. People are free to accept or reject them as they please, and
science has absolutely nothing to say on the subject. Science not only
rules out the acceptance of divine influence; it also rules out the
rejection of divine influence.
Evolution is not alone in its naturalism. All science, all
engineering, all manufacturing, and most other human endeavors are
equally naturalistic. If we must discard evolution because of this
philosophy, then we must also discard navigation, meteorology, farming,
architecture, printing, law, and virtually all other subjects for the
same reason.
Intelligent design implies philosophical naturalism. As noted above,
all science, industry, agriculture, and so forth is based on nature.
That does not stop evolutionists, other scientists, engineers,
manufacturers, and farmers from being able to look beyond the
materialism and find spirituality in their lives.
The intelligent design crowd, on the other hand, seems unable to make
that step. They seem to require objective, material evidence to back
up their spirituality. But that, of course, makes their spirituality
naturalistic. For all their complaints about materialism, people like
Dembski and Johnson are trying to expand materialism into the field
of religion.