Many religious people regard methodological materialism as an insult to religion, but it could be reasonably seen as an insult to atheism. Because it is irrational to sacrifice the infinite for the finite the rational individual will not commit herself to the pursuit of the finite objectives of materialism. Instead the rational individual will either search for the true religion, or try to live by what they believe, correctly or incorrectly, is the true religion. So it is precisely the weakness and irrationality of materialism that makes it useful as a neutral ground for scientific enquiry.
The use of methodological materialism as neutral ground for science is similar to the choice of small neutral countries for Cold War diplomacy. Finland, Austria, and Switzerland were all used in this way. The choice of Finland for the negotiations that produced the Helsinki accords was not based on Finland's power, but rather Finland’s lack of power. No rational individual would think that Finland was going to rule the world just because it was the host for the negotiations. In the same way it is materialism's weakness and irrationality that makes it so useful as a neutral ground for scientific study.
If we admit that methodological materialism is a social and institutional convention it may be easier for religious scientists, students, and the voters, to accept it. Just as it might be easier for religious people to accept that there need to be limits on religion in the public schools if we started by saying that religion is not excluded because it is wrong or unimportant, but precisely because religion is considered too important to be taught by mere government officials.
Who knows what stimulates the scientific researcher's thinking, and perhaps we should not care. If the scientist's hypothesis is confirmed by repeated experiments then, at least theoretically, that is what science requires.
While scientists commonly claim that one has to adopt methodological materialism to do science the truth is that much of the greatest scientific work started as an attempt to prove the existence of God using techniques normally associated with science. These discoveries were made through the exact opposite of methodological materialism.
For example, a Catholic clergyman, Copernicus, was trying to prove God's existence by showing that the earth and the other planets orbit the sun in perfect circles. He thought that perfectly circular orbits implied intelligent design. It did not work out, the planet's orbits are elliptical, but Copernicus is considered the father of modern science nevertheless.
Kepler discovered that the planets followed elliptical orbits. Like Copernicus, Kepler was using science in an attempt to prove the intelligent design of the solar system. His plan is too complex to explain here, but it did not work out. Nevertheless, Kepler also made a major discovery.
I believe Newton might also be added to this list. He thought angels kept the planets stable in their orbits, but it was discovered that the stability could be explained by natural means.
It could be reasonably argued that modern science was largely founded on a series of failed attempts to prove intelligent design.
Even in the twentieth century the Belgian priest, Georges Lemaitre, independently rediscovered the Big Bang theory that Soviet scientist Alekandr Friedmann had discovered previously. Friedmann failed to bring it to the attention of the scientific community, but Lamaitre did and was therefore called the father, if not exactly the discoverer, of the Big Bang. Father Lamaitre and the Catholic Church more generally liked the idea of the Big Bang because it suggested to them that God had created the universe on a "day without yesterday."
So perhaps the method, or at least the thinking that comes before the experiment, is not materialistic. Perhaps, it is just the presentation that is materialistic.
After all patriotism, religion, and perhaps other loyalties sometimes inspire scientific effort, so if we tolerate a little flag waving it maybe a cheap way to encourage scientific exploration.
The point of presentational materialism is simply that there is reason to avoid unnecessary mention of God in scientific discourse, and that my fellow religious people need not think this is a slight against their faith.
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