"A methodological naturalist believes that any deities or Intelligences not
visible in nature (which can be approached by methodological naturalism)
are unharmed."
"Not visible in nature" assumes that God is only visible in miracles, which
is not the view of many theists. I personally do not see how one can do
science without methodological naturalism, since there is the underlying
assumption of uniformitarianism and God's actions are not sufficiently
constrained to make that assumption. However, it is possible to see God's
hand in this predictability rather than simply accepting it as the way the
universe happens to work.
"But a methodological naturalist would analyse the birth of Jesus Christ
the same way as a philosophical naturalist. The methodological naturalist
would want to know what was the chromosome complement of Jesus, would want
to conduct some paternity testing, etc. The methodological naturalist is
just as great a menace to miracles that happen in the natural world. Or you
would have to call it, "methodological naturalism" plus as many exceptions
as your religion might require for miracles that occur in the natural
world."
Methodological naturalism, as its name implies, is a method. A miracle is
not an exception to methodological naturalism. Rather, it is an exception
to the assumption that methodological naturalism can explain the situation.
Methodological naturalism is no menace to miracles in the natural world;
instead, it may more fully document them. Given the limited equipment
available, Thomas can be viewed as something of a methodological
naturalist. He sought physical evidence as to what had happened, but was
unable to find a natural explanation for the evidence he saw. In the
example you cite, if unlimited resources were available, a methodologically
natural paternity analysis might show that no one was Jesus' father. That
is all that methodological naturalism could do in that case. Philosophical
naturalism would then claim that someone must have been missed in the
search for potential fathers, whereas other views would consider the
possibility that something supernatural happened.
David Campbell